+> Fix End of Files.........................................................Passed
+> Trim Trailing Whitespace.................................................Failed
+> - hook id: trailing-whitespace
+> - exit code: 1
+> - files were modified by this hook
+>
+> Fixing path/to/changed/files/file.txt
+>
+> codespell................................................................Passed
+> style-files..........................................(no files to check)Skipped
+> readme-rmd-rendered..................................(no files to check)Skipped
+> use-tidy-description.................................(no files to check)Skipped
+ +In the example above, one of the hooks modified a file in the proposed commit, +so the pre-commit check failed. You can run `git diff` to see the changes that +pre-commit made and `git status` to see which files were modified. To proceed +with the commit, re-add the modified file(s) and re-run the commit command: + +```sh +git add path/to/changed/files/file.txt +git commit -m 'feat: create function for awesome feature' +``` + +This time, all the hooks either passed or were skipped +(e.g. hooks that only run on R code will not run if no R files were +committed). +When the pre-commit check is successful, the usual commit success message +will appear after the pre-commit messages showing that the commit was created. + +> Check for added large files..............................................Passed
+> Fix End of Files.........................................................Passed
+> Trim Trailing Whitespace.................................................Passed
+> codespell................................................................Passed
+> style-files..........................................(no files to check)Skipped
+> readme-rmd-rendered..................................(no files to check)Skipped
+> use-tidy-description.................................(no files to check)Skipped
+> Conventional Commit......................................................Passed
+> [iss-10 9ff256e] feat: create function for awesome feature
+> 1 file changed, 22 insertions(+), 3 deletions(-)
+ +Finally, push your changes to GitHub: + +```sh +git push +``` + +If this is the first time you are pushing this branch, you may have to +explicitly set the upstream branch: + +```sh +git push --set-upstream origin iss-10 +``` + +> Enumerating objects: 7, done.
+> Counting objects: 100% (7/7), done.
+> Delta compression using up to 10 threads
+> Compressing objects: 100% (4/4), done.
+> Writing objects: 100% (4/4), 648 bytes | 648.00 KiB/s, done.
+> Total 4 (delta 3), reused 0 (delta 0), pack-reused 0
+> remote: Resolving deltas: 100% (3/3), completed with 3 local objects.
+> remote:
+> remote: Create a pull request for 'iss-10' on GitHub by visiting:
+> remote: https://github.com/CCBR/MOSuite/pull/new/iss-10
+> remote:
+> To https://github.com/CCBR/MOSuite
+>
+> [new branch] iss-10 -> iss-10
+> branch 'iss-10' set up to track 'origin/iss-10'.
+ +We recommend pushing your commits often so they will be backed up on GitHub. +You can view the files in your branch on GitHub at +`https://github.com/CCBR/MOSuite/tree/
change_threshold:", + df[[lfc_name]], + "
P-value:", + df[[sig_name]] + ), + colour = as.character(plot_data$colour), + fill = as.character(plot_data$colour) # Set fill to the same as colour + ), + shape = 21, + # Shape that supports both colour and fill + size = 2, + # Size of the points + stroke = 0.1 # Stroke width + ) + + ggplot2::scale_fill_identity() + + # Add interactive hover labels for the gene names + volcano_plot <- plotly::ggplotly(pxx, tooltip = c("text")) + } + plots_list[[i]] <- volcano_plot + } + plot_patchwork <- patchwork::wrap_plots(plots_list) + print_or_save_plot( + plot_patchwork, + filename = file.path(plots_subdir, plot_filename), + print_plots = print_plots, + save_plots = save_plots, + units = "px", + width = image_width, + height = image_height, + dpi = dpi + ) + + df_final <- cbind(diff_dat, do.call(cbind, rank)) + return(df_final) +} diff --git a/code/MOSuite/R/plot_volcano_summary.R b/code/MOSuite/R/plot_volcano_summary.R new file mode 100644 index 0000000..92a50f3 --- /dev/null +++ b/code/MOSuite/R/plot_volcano_summary.R @@ -0,0 +1,539 @@ +#' Volcano Plot - Summary +#' +#' Produces one volcano plot for each tested contrast in the input DEG table. +#' It can be sorted by either fold change, t-statistic, or p-value. The returned dataset includes one row for each +#' significant gene in each contrast, and contains columns from the DEG analysis of that contrast as well as columns +#' useful to the Venn diagram template downstream. +#' An S7 generic with methods for `multiOmicDataSet` and `data.frame`. +#' +#' @param moo_diff multiOmicDataSet or differential expression analysis result data frame. +#' +#' @export +plot_volcano_summary <- S7::new_generic( + "plot_volcano_summary", + "moo_diff", + function( + moo_diff, + feature_id_colname = NULL, + signif_colname = "pval", + signif_threshold = 0.05, + change_threshold = 1, + value_to_sort_the_output_dataset = "t-statistic", + num_features_to_label = 30, + add_features = FALSE, + label_features = FALSE, + custom_gene_list = "", + default_label_color = "black", + custom_label_color = "green3", + label_x_adj = 0.2, + label_y_adj = 0.2, + line_thickness = 0.5, + label_font_size = 4, + label_font_type = 1, + displace_feature_labels = FALSE, + custom_gene_list_special_label_displacement = "", + special_label_displacement_x_axis = 2, + special_label_displacement_y_axis = 2, + color_of_signif_threshold_line = "blue", + color_of_non_significant_features = "black", + color_of_logfold_change_threshold_line = "red", + color_of_features_meeting_only_signif_threshold = "lightgoldenrod2", + color_for_features_meeting_pvalue_and_foldchange_thresholds = "red", + flip_vplot = FALSE, + use_default_x_axis_limit = TRUE, + x_axis_limit = 5, + use_default_y_axis_limit = TRUE, + y_axis_limit = 10, + point_size = 2, + add_deg_columns = c("FC", "logFC", "tstat", "pval", "adjpval"), + graphics_device = grDevices::png, + image_width = 15, + image_height = 15, + dpi = 300, + use_default_grid_layout = TRUE, + number_of_rows_in_grid_layout = 1, + aspect_ratio = 0, + plot_filename = "volcano_summary.png", + print_plots = options::opt("print_plots"), + save_plots = options::opt("save_plots"), + plots_subdir = "diff" + ) { + return(S7::S7_dispatch()) + } +) + +#' @rdname plot_volcano_summary +S7::method(plot_volcano_summary, multiOmicDataSet) <- function( + moo_diff, + feature_id_colname = NULL, + signif_colname = "pval", + signif_threshold = 0.05, + change_threshold = 1, + value_to_sort_the_output_dataset = "t-statistic", + num_features_to_label = 30, + add_features = FALSE, + label_features = FALSE, + custom_gene_list = "", + default_label_color = "black", + custom_label_color = "green3", + label_x_adj = 0.2, + label_y_adj = 0.2, + line_thickness = 0.5, + label_font_size = 4, + label_font_type = 1, + displace_feature_labels = FALSE, + custom_gene_list_special_label_displacement = "", + special_label_displacement_x_axis = 2, + special_label_displacement_y_axis = 2, + color_of_signif_threshold_line = "blue", + color_of_non_significant_features = "black", + color_of_logfold_change_threshold_line = "red", + color_of_features_meeting_only_signif_threshold = "lightgoldenrod2", + color_for_features_meeting_pvalue_and_foldchange_thresholds = "red", + flip_vplot = FALSE, + use_default_x_axis_limit = TRUE, + x_axis_limit = 5, + use_default_y_axis_limit = TRUE, + y_axis_limit = 10, + point_size = 2, + add_deg_columns = c("FC", "logFC", "tstat", "pval", "adjpval"), + graphics_device = grDevices::png, + image_width = 15, + image_height = 15, + dpi = 300, + use_default_grid_layout = TRUE, + number_of_rows_in_grid_layout = 1, + aspect_ratio = 0, + plot_filename = "volcano_summary.png", + print_plots = options::opt("print_plots"), + save_plots = options::opt("save_plots"), + plots_subdir = "diff" +) { + return( + moo_diff@analyses$diff |> + join_dfs_wide() |> + plot_volcano_summary( + feature_id_colname, + signif_colname, + signif_threshold, + change_threshold, + value_to_sort_the_output_dataset, + num_features_to_label, + add_features, + label_features, + custom_gene_list, + default_label_color, + custom_label_color, + label_x_adj, + label_y_adj, + line_thickness, + label_font_size, + label_font_type, + displace_feature_labels, + custom_gene_list_special_label_displacement, + special_label_displacement_x_axis, + special_label_displacement_y_axis, + color_of_signif_threshold_line, + color_of_non_significant_features, + color_of_logfold_change_threshold_line, + color_of_features_meeting_only_signif_threshold, + color_for_features_meeting_pvalue_and_foldchange_thresholds, + flip_vplot, + use_default_x_axis_limit, + x_axis_limit, + use_default_y_axis_limit, + y_axis_limit, + point_size, + add_deg_columns, + graphics_device, + image_width, + image_height, + dpi, + use_default_grid_layout, + number_of_rows_in_grid_layout, + aspect_ratio, + plot_filename, + print_plots, + save_plots, + plots_subdir + ) + ) +} + +#' @inheritParams option_params +#' @inheritParams plot_volcano_enhanced +#' @inheritParams filter_counts +#' +#' @param add_features Add custom_gene_list To Labels. Set TRUE when you want to label a specific set of features +#' (features) in the "custom_gene_list" parameter" IN ADDITION to the number of features you set in the "Number of +#' Features to Label" parameter. +#' @param label_features Select TRUE when you want to label ONLY a specific list of features(features) given in the +#' "custom_gene_list" parameter. +#' @param custom_gene_list Provide a list of features (comma separated) to be labeled on the volcano plot. You must +#' toggle one of the following ON to see these labels: "Add features" or "Label Only My Feature List". +#' @param default_label_color Set the color for the text used to add feature (gene) name labels to points. +#' @param custom_label_color Set the color for the specific list of features (features) provided in the "Feature List" +#' parameter. +#' @param label_x_adj adjust position of the labels on the x-axis. Default: 0.2 +#' @param label_y_adj adjust position of the labels on the y-axis. Default: 0.2 +#' @param line_thickness Set the thickness of the lines in the plot. Default: 0.5 +#' @param label_font_size Set the font size of the labels. Default: 4 +#' @param label_font_type Set the font type of the labels. Default: 1 +#' @param displace_feature_labels Set to TRUE to displace gene labels. Default: FALSE. Set TRUE if you want to displace +#' the feature (gene) label for a specific set of features. Make sure to use custom x- and y- limits and give +#' sufficient space for displacement; otherwise other labels than the desired ones will appear displaced. +#' @param custom_gene_list_special_label_displacement Provide a list of features (comma separated) for which you want +#' special displacement of the feature label. +#' @param special_label_displacement_x_axis Displacement of the feature label on the x-axis. Default: 2 +#' @param special_label_displacement_y_axis Displacement of the feature label on the y-axis. Default: 2 +#' @param color_of_signif_threshold_line Color of the significance threshold line. Default: "blue" +#' @param color_of_non_significant_features Color of the non-significant features. Default: "black" +#' @param color_of_logfold_change_threshold_line Color of the log fold change threshold line. Default: "red" +#' @param color_of_features_meeting_only_signif_threshold Color of the features that meet only the significance +#' threshold. Default: "lightgoldenrod2" +#' @param color_for_features_meeting_pvalue_and_foldchange_thresholds Color of the features that meet both the p-value +#' and fold change thresholds. Default: "red" +#' @param flip_vplot Set to TRUE to flip the fold change values so that the volcano plot looks like a comparison was +#' B-A. Default: FALSE +#' @param use_default_x_axis_limit Set to TRUE to use the default x-axis limit. Default: TRUE +#' @param x_axis_limit Custom x-axis limit. Default: c(-5, 5) +#' @param use_default_y_axis_limit Set to TRUE to use the default y-axis limit. Default: TRUE +#' @param y_axis_limit Custom y-axis limit. Default: c(0, 10) +#' @param point_size Size of the points in the plot. Default: 1 +#' @param add_deg_columns Add additional columns from the DEG analysis to the +#' output dataset. Default: `"FC", "logFC", "tstat", "pval", "adjpval"` +#' @param use_default_grid_layout Set to TRUE to use the default grid layout. Default: TRUE +#' @param number_of_rows_in_grid_layout Number of rows in the grid layout. Default: 1 +#' @param aspect_ratio Aspect ratio of the output image. Default: 4/3 +#' @param graphics_device passed to `ggsave(device)`. Default: `grDevices::png` +#' @param plot_filename Filename for the output plot. Default: "volcano_plot.png" +#' +#' @keywords plotters volcano +#' +#' @examples +#' plot_volcano_summary(nidap_deg_analysis, print_plots = TRUE) +#' +#' @rdname plot_volcano_summary +#' +S7::method(plot_volcano_summary, S7::class_data.frame) <- function( + moo_diff, + feature_id_colname = NULL, + signif_colname = "pval", + signif_threshold = 0.05, + change_threshold = 1, + value_to_sort_the_output_dataset = "t-statistic", + num_features_to_label = 30, + add_features = FALSE, + label_features = FALSE, + custom_gene_list = "", + default_label_color = "black", + custom_label_color = "green3", + label_x_adj = 0.2, + label_y_adj = 0.2, + line_thickness = 0.5, + label_font_size = 4, + label_font_type = 1, + displace_feature_labels = FALSE, + custom_gene_list_special_label_displacement = "", + special_label_displacement_x_axis = 2, + special_label_displacement_y_axis = 2, + color_of_signif_threshold_line = "blue", + color_of_non_significant_features = "black", + color_of_logfold_change_threshold_line = "red", + color_of_features_meeting_only_signif_threshold = "lightgoldenrod2", + color_for_features_meeting_pvalue_and_foldchange_thresholds = "red", + flip_vplot = FALSE, + use_default_x_axis_limit = TRUE, + x_axis_limit = 5, + use_default_y_axis_limit = TRUE, + y_axis_limit = 10, + point_size = 2, + add_deg_columns = c("FC", "logFC", "tstat", "pval", "adjpval"), + graphics_device = grDevices::png, + image_width = 15, + image_height = 15, + dpi = 300, + use_default_grid_layout = TRUE, + number_of_rows_in_grid_layout = 1, + aspect_ratio = 0, + plot_filename = "volcano_summary.png", + print_plots = options::opt("print_plots"), + save_plots = options::opt("save_plots"), + plots_subdir = "diff" +) { + abort_packages_not_installed("patchwork", "ggrepel") + diff_dat <- as.data.frame(moo_diff) + + ## -------------------------------- ## + ## User-Defined Template Parameters ## + ## -------------------------------- ## + ### PH + # Input - DEG table from Limma DEG template + # Output - Venn Diagrams for selected Comparisons + + # Simplified DEG table for selected Comparisons (Only used for Venn Diagram) + # Purpose - Create Multiple Venn Diagrams + # Can we use Visualizations from Advanced Volcano function used in the stand alone Volcano plot? + + # Basic Parameters: + if (is.null(feature_id_colname)) { + feature_id_colname <- colnames(diff_dat)[1] + } + + # Identify all contrasts in DEG output table + volcols <- colnames(diff_dat) + statcols <- volcols[grepl("logFC", volcols)] + contrasts <- unique(gsub("_logFC", "", statcols)) + + Plots <- list() + df_outs <- list() + + # Create Volcano for each DEG comparison + for (contrast in contrasts) { + ### PH: START Build table for Volcano plot + message(paste0("Preparing table for contrast: ", contrast)) + lfccol <- paste0(contrast, "_logFC") + pvalcol <- paste0(contrast, "_", signif_colname) + tstatcol <- paste0(contrast, "_", "tstat") + + message(paste0("Fold change column: ", lfccol)) + message(paste0(signif_colname, " column: ", pvalcol)) + + if (value_to_sort_the_output_dataset == "fold-change") { + diff_dat <- diff_dat |> + dplyr::arrange(dplyr::desc(abs(diff_dat[, lfccol]))) + } else if (value_to_sort_the_output_dataset == "p-value") { + diff_dat <- diff_dat |> dplyr::arrange(diff_dat[, pvalcol]) + } else if (value_to_sort_the_output_dataset == "t-statistic") { + diff_dat <- diff_dat |> + dplyr::arrange(dplyr::desc(abs(diff_dat[, tstatcol]))) + } + + ## optional Parameter: Provide a list of features to label on Volcano plot + ## work with a list of features + if (add_features == TRUE) { + gl <- trimws( + unlist(strsplit( + c( + custom_gene_list + ), + "," + )), + which = c("both") + ) + ind <- match(gl, diff_dat$Gene) # get the indices of the listed features + custom_gene_list_ind <- c(1:num_features_to_label, ind) # when list provided + color_gene_label <- c( + rep(c(default_label_color), num_features_to_label), + rep(c(custom_label_color), length(ind)) + ) + } else if (label_features == TRUE) { + gl <- trimws( + unlist(strsplit( + c( + custom_gene_list + ), + "," + )), + which = c("both") + ) # unpack the gene list provided by the user and remove white spaces + ind <- match(gl, diff_dat$Gene) # get the indices of the listed features + custom_gene_list_ind <- ind # when list provided + color_gene_label <- rep(c(custom_label_color), length(ind)) + } else { + if (num_features_to_label > 0) { + # if no list provided label the number of features given by the user + custom_gene_list_ind <- 1:num_features_to_label + color_gene_label <- rep(c(default_label_color), num_features_to_label) + } else if (num_features_to_label == 0) { + custom_gene_list_ind <- 0 + } + } + + ## optional Parameter: IF DEG was set up A-B User can Flip FC values so that Volcano plot looks like comparison was + ## B-A + ## flip contrast section + indc <- which(colnames(diff_dat) == lfccol) # get the indice of the column that contains the contrast_logFC data + + if (length(indc) == 0) { + message( + "Please rename the logFC column to include the contrast evaluated." + ) + } else { + old_contrast <- colnames(diff_dat)[indc] + } + # actually flip contrast + if (flip_vplot == TRUE) { + # get the indice of the contrast to flip + indcc <- match(old_contrast, colnames(diff_dat)) + # create flipped contrast label + splt1 <- strsplit(old_contrast, "_") # split by underline symbol to isolate the contrast name + splt2 <- strsplit(splt1[[1]][1], "-") # split the contrast name in the respective components + flipped_contrast <- paste(splt2[[1]][2], splt2[[1]][1], sep = "-") # flip contrast name + new_contrast_label <- paste(flipped_contrast, c("logFC"), sep = "_") + # rename contrast column to the flipped contrast + colnames(diff_dat)[indcc] <- new_contrast_label + # flip the contrast data around y-axis + diff_dat[, indcc] <- -diff_dat[indcc] + } else { + new_contrast_label <- old_contrast + } + + filtered_features <- diff_dat$Gene[ + diff_dat[, pvalcol] < signif_threshold & + abs(diff_dat[, new_contrast_label]) > change_threshold + ] + repeated_column <- rep(contrast, length(filtered_features)) + + ## If param empty or FALSE, fill it with default value. + if ( + is.null(add_deg_columns) || + length(add_deg_columns) == 0 || + isFALSE(add_deg_columns) + ) { + add_deg_columns <- c("FC", "logFC", "tstat", "pval", "adjpval") + } + + if (all(add_deg_columns == "none")) { + new_df <- data.frame(filtered_features, repeated_column) + names(new_df) <- c(feature_id_colname, "Contrast") + } else { + add_deg_columns <- setdiff(add_deg_columns, "none") + out_columns <- paste(contrast, add_deg_columns, sep = "_") + deg <- diff_dat[, c(feature_id_colname, out_columns)] + names(deg)[1] <- feature_id_colname + new_df <- data.frame(filtered_features, repeated_column) |> + dplyr::left_join(deg, by = c("filtered_features" = feature_id_colname)) + names(new_df) <- c(feature_id_colname, "Contrast", add_deg_columns) + } + + df_out1 <- new_df + df_outs[[contrast]] <- df_out1 + + ### PH: END Build table for Volcano plot + + ### PH: START Make plot - Can we use Enhanced volcano function from other template to make figure instead of ggplot + ### shown here + + message(paste0( + "Total number of features included in volcano plot: ", + nrow(diff_dat) + )) + ## special nudge/repel of specific features + if (displace_feature_labels) { + gn <- trimws( + unlist(strsplit( + c(custom_gene_list_special_label_displacement), + "," + )), + which = c("both") + ) + ind_gn <- match(gn, diff_dat$Gene[custom_gene_list_ind]) # get the indices of the listed features + nudge_x_all <- rep(c(0.2), length(diff_dat$Gene[custom_gene_list_ind])) + nudge_y_all <- rep(c(0.2), length(diff_dat$Gene[custom_gene_list_ind])) + nudge_x_all[ind_gn] <- c(special_label_displacement_x_axis) + nudge_y_all[ind_gn] <- c(special_label_displacement_y_axis) + } else { + nudge_x_all <- label_x_adj + nudge_y_all <- label_y_adj + } + + # set plot parameters + if (use_default_y_axis_limit) { + negative_log10_p_values <- -log10(diff_dat[, pvalcol]) + ymax <- ceiling(max(negative_log10_p_values[is.finite( + negative_log10_p_values + )])) + } else { + ymax <- y_axis_limit + } + if (use_default_x_axis_limit) { + xmax1 <- ceiling(max(diff_dat[, lfccol])) + xmax2 <- ceiling(max(-diff_dat[, lfccol])) + xmax <- max(xmax1, xmax2) + } else { + xmax <- x_axis_limit + } + + grm <- diff_dat[, c(new_contrast_label, pvalcol)] + grm[, "neglogpval"] <- -log10(diff_dat[, pvalcol]) + colnames(grm) <- c("FC", "pval", "neglogpval") + # message(grm[custom_gene_list_ind, ]) + p <- ggplot2::ggplot( + grm, + ggplot2::aes( + x = !!rlang::sym("FC"), + y = !!rlang::sym("neglogpval") + ) + ) + # modified by RAS + ggplot2::theme_classic() + + ggplot2::geom_point( + color = color_of_non_significant_features, + size = point_size + ) + + ggplot2::geom_vline( + xintercept = c(-change_threshold, change_threshold), + color = color_of_logfold_change_threshold_line, + alpha = 1.0 + ) + + ggplot2::geom_hline( + yintercept = -log10(signif_threshold), + color = color_of_signif_threshold_line, + alpha = 1.0 + ) + + ggplot2::geom_point( + data = grm[diff_dat[, pvalcol] < signif_threshold, ], + color = color_of_features_meeting_only_signif_threshold, + size = point_size + ) + + ggplot2::geom_point( + data = grm[ + diff_dat[, pvalcol] < signif_threshold & + abs(grm[, "FC"]) > change_threshold, + ], + color = color_for_features_meeting_pvalue_and_foldchange_thresholds, + size = point_size + ) + + ggrepel::geom_text_repel( + data = grm[custom_gene_list_ind, ], + label = diff_dat$Gene[custom_gene_list_ind], + color = color_gene_label, + fontface = label_font_type, + nudge_x = nudge_x_all, + nudge_y = nudge_y_all, + size = label_font_size, + segment.size = line_thickness + ) + + ggplot2::xlim(-xmax, xmax) + + ggplot2::ylim(0, ymax) + + ggplot2::xlab(new_contrast_label) + + ggplot2::ylab(pvalcol) + + if (aspect_ratio > 0) { + p <- p + ggplot2::coord_fixed(ratio = aspect_ratio) + } + + Plots[[contrast]] <- p + ### PH: END Make plot - Can we use Enhanced volcano function from other template to make figure instead of ggplot + ### shown here + } + + ## Print plots + nplots <- length(Plots) + if (use_default_grid_layout) { + nrows <- ceiling(nplots / ceiling(sqrt(nplots))) + } else { + nrows <- number_of_rows_in_grid_layout + } + plot_patchwork <- patchwork::wrap_plots(Plots, nrow = nrows) + print_or_save_plot( + plot_patchwork, + filename = file.path(plots_subdir, plot_filename), + print_plots = print_plots, + save_plots = save_plots, + graphics_device = graphics_device + ) + + df_out <- unique(do.call("rbind", df_outs)) + + return(df_out) +} diff --git a/code/MOSuite/R/plots.R b/code/MOSuite/R/plots.R new file mode 100644 index 0000000..c814b78 --- /dev/null +++ b/code/MOSuite/R/plots.R @@ -0,0 +1,52 @@ +#' Print and/or save a ggplot +#' +#' If `save_plots` is `TRUE`, the plot will be saved as an image to the path at +#' `file.path(plots_dir, filename)`. +#' If `plot_obj` is a ggplot, `ggplot2::ggsave()` is used to save the image. +#' Otherwise, `graphics_device` is used (`grDevice::png()` by default). +#' +#' @inheritParams option_params +#' @param plot_obj plot object (e.g. ggplot, ComplexHeatmap...) +#' @param filename name of the output file. will be joined with the `plots_dir` option. +#' @param graphics_device Default: `grDevice::png()`. Only used if the plot is not a ggplot. +#' @param ... arguments forwarded to `ggplot2::ggsave()` +#' +#' @return invisibly returns the path where the plot image was saved to the disk +#' @export +#' @family plotters +#' @keywords plotters +print_or_save_plot <- function( + plot_obj, + filename, + print_plots = options::opt("print_plots"), + save_plots = options::opt("save_plots"), + plots_dir = options::opt("plots_dir"), + graphics_device = grDevices::png, + ... +) { + if (isTRUE(print_plots)) { + print(plot_obj) + } + if (isTRUE(save_plots)) { + # create output directory if it doesn't exist + if (!is.null(plots_dir) && nchar(plots_dir) > 0) { + filename <- file.path(plots_dir, filename) + } + outdir <- dirname(filename) + if (!dir.exists(outdir)) { + dir.create(outdir, recursive = TRUE) + } + + # select saving methods depending on plot object class + if (inherits(plot_obj, "ggplot")) { + ggplot2::ggsave(filename = filename, plot = plot_obj, ...) + } else if (inherits(plot_obj, "htmlwidget")) { + htmlwidgets::saveWidget(plot_obj, filename, ...) + } else { + graphics_device(file = filename) + plot(plot_obj) + grDevices::dev.off() + } + } + return(invisible(filename)) +} diff --git a/code/MOSuite/R/reexports.R b/code/MOSuite/R/reexports.R new file mode 100644 index 0000000..c7c32ad --- /dev/null +++ b/code/MOSuite/R/reexports.R @@ -0,0 +1,20 @@ +#' walrus operator +#' @importFrom rlang := +#' @export +rlang::`:=` + +#' bang-bang +#' @importFrom rlang !! +#' @export +rlang::`!!` + +#' rlang data pronoun +#' @importFrom rlang .data +#' @export +rlang::.data + +# Suppress R CMD check note 'All declared Imports should be used'. +# These are used in S7 methods. +#' @importFrom dendextend rotate +#' @importFrom matrixStats rowVars +NULL diff --git a/code/MOSuite/R/rename.R b/code/MOSuite/R/rename.R new file mode 100644 index 0000000..065af00 --- /dev/null +++ b/code/MOSuite/R/rename.R @@ -0,0 +1,31 @@ +#' Rename samples +#' +#' TODO this should happen right at the beginning of the template? +#' +#' TODO accept new names for samples in sample metadata spreadsheet +#' +#' +#' @param dat data frame +#' @param samples_to_rename_manually TODO use sample metadata spreadsheet custom column. Need to document the format of +#' this object. +#' +#' @return data frame with samples renamed +#' @keywords internal +#' +rename_samples <- function(dat, samples_to_rename_manually) { + replacements <- samples_to_rename_manually + + if ( + !is.null(replacements) && + (length(replacements) > 0) && + (nchar(replacements) > 0) + ) { + # TODO: refactor with dplyr::rename for simplicity + for (x in replacements) { + old <- strsplit(x, ": ?")[[1]][1] + new <- strsplit(x, ": ?")[[1]][2] + colnames(dat)[colnames(dat) %in% old] <- new + } + } + return(dat) +} diff --git a/code/MOSuite/R/utils.R b/code/MOSuite/R/utils.R new file mode 100644 index 0000000..8d7106c --- /dev/null +++ b/code/MOSuite/R/utils.R @@ -0,0 +1,332 @@ +#' Glue gene_id and GeneName columns into one column +#' +#' @param counts_dat data frame containing gene_id and GeneName columns +#' +#' @returns counts_dat with gene_id and GeneName joined with `|` as the new gene_id column +#' @keywords internal +#' @examples +#' \dontrun{ +#' gene_counts |> +#' glue_gene_symbols() |> +#' head() +#' } +glue_gene_symbols <- function(counts_dat) { + if ( + "gene_id" %in% colnames(counts_dat) && "GeneName" %in% colnames(counts_dat) + ) { + counts_dat <- counts_dat |> + dplyr::mutate( + gene_id = glue::glue("{gene_id}|{GeneName}"), + .keep = "unused" + ) + } + return(counts_dat) +} + +#' Check whether package(s) are installed +#' +#' @param ... names of packages to check +#' @return named vector with status of each packages; installed (`TRUE`) or not (`FALSE`) +#' @keywords internal +#' +#' @examples +#' \dontrun{ +#' check_packages_installed("base") +#' check_packages_installed("not-a-package-name") +#' all(check_packages_installed("parallel", "doFuture")) +#' } +check_packages_installed <- function(...) { + return(sapply(c(...), requireNamespace, quietly = TRUE)) +} + +#' Throw error if required packages are not installed. +#' +#' Reports which packages need to be installed and the parent function name. +#' See +#' https://stackoverflow.com/questions/15595478/how-to-get-the-name-of-the-calling-function-inside-the-called-routine +#' +#' @inheritParams check_packages_installed +#' @keywords internal +#' +#' @examples +#' \dontrun{ +#' abort_packages_not_installed("base") +#' abort_packages_not_installed("not-a-package-name", "caret", "dplyr", "non_package") +#' } +abort_packages_not_installed <- function(...) { + package_status <- check_packages_installed(...) + packages_not_installed <- Filter(isFALSE, package_status) + if (length(packages_not_installed) > 0) { + msg <- paste0( + "The following package(s) are required but are not installed: \n ", + paste0(names(packages_not_installed), collapse = ", ") + ) + stop(msg) + } +} + +#' Function for testing CLI argument parsing +#' +#' @param add whether to add left and right +#' @param subtract whether to subtract left and right +#' @param left number on the left side of the operand +#' @param right number on the right side of the operand +#' +#' @returns result of adding or subtracting left and right +#' +#' @export +#' @keywords internal +do_math <- function(add = TRUE, subtract = FALSE, left = 1, right = 2) { + result <- NULL + if (isTRUE(add)) { + result <- left + right + } else if (isTRUE(subtract)) { + result <- left - right + } + return(result) +} + +#' Join dataframes in named list to wide dataframe +#' +#' The first column is assumed to be shared by all dataframes +#' +#' @param df_list named list of dataframes +#' @param join_fn join function to use (Default: `dplyr::left_join`) +#' +#' @returns wide dataframe +#' @export +#' @keywords utilities +#' +#' @examples +#' +#' dfs <- list( +#' "a_vs_b" = data.frame(id = c("a1", "b2", "c3"), score = runif(3)), +#' "b_vs_c" = data.frame(id = c("a1", "b2", "c3"), score = rnorm(3)) +#' ) +#' dfs |> join_dfs_wide() +#' +join_dfs_wide <- function(df_list, join_fn = dplyr::left_join) { + if (!inherits(df_list, "list")) { + stop(glue::glue("df_list must be a named list. class: {class(df_list)}")) + } + if (is.null(names(df_list))) { + stop(glue::glue("df_list does not have names")) + } + # use first column as start + common_col <- df_list[[1]] |> + dplyr::select(1) |> + colnames() + dat_joined <- purrr::map(names(df_list), \(df_name) { + result <- df_list[[df_name]] |> + dplyr::rename_with( + .cols = !tidyselect::any_of(common_col), + .fn = \(x) { + return(glue::glue("{df_name}_{x}")) + } + ) + return(result) + }) |> + purrr::reduce(join_fn) + return(dat_joined) +} + +#' Bind dataframes in named list to long dataframe +#' +#' The dataframes must have all of the same columns +#' +#' @param df_list named list of dataframes +#' @param outcolname column name in output dataframe for the names from the named list +#' +#' @returns long dataframe with new column `outcolname` from named list +#' @export +#' @keywords utilities +#' +#' @examples +#' +#' dfs <- list( +#' "a_vs_b" = data.frame(id = c("a1", "b2", "c3"), score = runif(3)), +#' "b_vs_c" = data.frame(id = c("a1", "b2", "c3"), score = rnorm(3)) +#' ) +#' dfs |> bind_dfs_long() +#' +bind_dfs_long <- function(df_list, outcolname = contrast) { + contrast <- NULL # data variable + if (!inherits(df_list, "list")) { + stop(glue::glue("df_list must be a named list. class: {class(df_list)}")) + } + if (is.null(names(df_list))) { + stop(glue::glue("df_list does not have names")) + } + # use first column as start + common_col <- df_list[[1]] |> + dplyr::select(1) |> + colnames() + dat_joined <- purrr::map(names(df_list), \(df_name) { + result <- df_list[[df_name]] |> + dplyr::mutate({{ outcolname }} := df_name, .after = common_col) + return(result) + }) |> + dplyr::bind_rows() + return(dat_joined) +} + +#' Set up capsule environment and directories +#' +#' Initializes the results directory structure and logs installed R package versions. +#' This is a common setup task used across all Code Ocean capsules. +#' +#' @param base_results_dir base path to results directory (default: `../results`) +#' +#' @returns invisibly returns a list with `results_dir` and `plots_dir` paths +#' @keywords internal +#' +#' @examples +#' \dontrun{ +#' setup_capsule_environment() +#' } +#' +#' @export +setup_capsule_environment <- function( + base_results_dir = file.path("..", "results") +) { + results_dir <- base_results_dir + plots_dir <- file.path(results_dir, "figures") + + # Set options for plots directory + options(moo_plots_dir = plots_dir, moo_save_plots = TRUE) + + # Log installed packages & versions + pkg_versions <- tibble::as_tibble(utils::installed.packages()) + readr::write_csv(pkg_versions, file.path(results_dir, "r-packages.csv")) + + return(invisible(list(results_dir = results_dir, plots_dir = plots_dir))) +} + +#' Load multiOmicDataSet from data directory +#' +#' Searches the ../data directory for .rds files and loads the first matching +#' multiOmicDataSet object. Validates that the loaded object is of the correct class. +#' +#' @param data_dir path to data directory containing .rds file (default: `../data`) +#' +#' @returns loaded multiOmicDataSet object +#' @keywords internal +#' +#' @examples +#' \dontrun{ +#' moo <- load_moo_from_data_dir() +#' } +#' +#' @export +load_moo_from_data_dir <- function(data_dir = file.path("..", "data")) { + regex_moo <- ".*\\.rds$" + data_files <- list.files(data_dir, recursive = TRUE, full.names = TRUE) + moo_files <- Filter( + \(x) stringr::str_detect(x, stringr::regex(regex_moo, ignore_case = TRUE)), + data_files + ) + + if (length(moo_files) == 0) { + stop(glue::glue("No files matching regex: {regex_moo}")) + } + + moo_filename <- moo_files[1] + moo <- readr::read_rds(moo_filename) + + message(glue::glue("Reading multiOmicDataSet from {moo_filename}")) + + if (!inherits(moo, "MOSuite::multiOmicDataSet")) { + stop(glue::glue("The input is not a multiOmicDataSet. class: {class(moo)}")) + } + + return(moo) +} + +#' Parse comma-separated string into a vector +#' +#' Splits a comma-separated string into a trimmed character vector. +#' Returns NULL if input is empty, NULL, or has zero length. +#' +#' @param x character string with comma-separated values +#' +#' @returns character vector or NULL if input is empty +#' @keywords internal +#' +#' @examples +#' \dontrun{ +#' parse_optional_vector("a, b, c") +#' parse_optional_vector("") +#' } +#' +#' @export +parse_optional_vector <- function(x) { + if (is.null(x) || identical(x, "") || length(x) == 0) { + return(NULL) + } + return(trimws(unlist(strsplit(x, ",")))) +} + +#' Parse comma-separated string with default fallback +#' +#' Splits a comma-separated string into a trimmed character vector. +#' Returns a default value if input is empty, NULL, or has zero length. +#' +#' @param x character string with comma-separated values +#' @param default default value to return if x is empty +#' +#' @returns character vector or default value +#' @keywords internal +#' +#' @examples +#' \dontrun{ +#' parse_vector_with_default("a, b, c", "default") +#' parse_vector_with_default("", "default") +#' } +#' +#' @export +parse_vector_with_default <- function(x, default) { + parsed <- parse_optional_vector(x) + if (is.null(parsed)) { + return(default) + } + return(parsed) +} + +#' Parse sample rename pairs from string +#' +#' Parses a string containing sample rename pairs in format "old:new,old2:new2" +#' and returns a named list where names are old sample names and values are new names. +#' +#' @param x character string with rename pairs in format "old:new,old2:new2" +#' +#' @returns named list with old names as keys and new names as values, or NULL if empty +#' @keywords internal +#' +#' @examples +#' \dontrun{ +#' parse_samples_to_rename("sample1:S1,sample2:S2") +#' parse_samples_to_rename("") +#' } +#' +#' @export +parse_samples_to_rename <- function(x) { + if (is.null(x) || identical(x, "") || length(x) == 0) { + return(NULL) + } + + pairs <- trimws(unlist(strsplit(x, ","))) + result <- list() + + for (pair in pairs) { + parts <- trimws(unlist(strsplit(pair, ":"))) + if (length(parts) == 2) { + result[[parts[1]]] <- parts[2] + } + } + + if (length(result) == 0) { + return(NULL) + } + + return(result) +} diff --git a/code/MOSuite/R/zzz.R b/code/MOSuite/R/zzz.R new file mode 100644 index 0000000..31a395d --- /dev/null +++ b/code/MOSuite/R/zzz.R @@ -0,0 +1,28 @@ +# source: https://rconsortium.github.io/S7/articles/packages.html#method-registration +.onLoad <- function(...) { + S7::methods_register() + + # necessary because moo_save_plots defaults to TRUE, causing figures to be + # written during R CMD check + is_r_cmd_check <- nzchar(Sys.getenv("_R_CHECK_PACKAGE_NAME_")) || + identical(tolower(Sys.getenv("R_CMD_CHECK")), "true") || + identical(tolower(Sys.getenv("R CMD check")), "true") + if ( + is_r_cmd_check && + is.null(getOption("moo_save_plots")) && + !nzchar(Sys.getenv("MOO_SAVE_PLOTS")) + ) { + options(moo_save_plots = FALSE) + } +} + +# enable usage of
+
+R package for differential multi-omics analysis
+
+
+[](https://github.com/CCBR/MOSuite/actions/workflows/R-CMD-check.yaml)
+[](https://codecov.io/gh/CCBR/MOSuite)
+[](https://github.com/CCBR/MOSuite/actions/workflows/github-code-scanning/codeql)
+[](https://github.com/CCBR/MOSuite/releases/latest)
+[](https://hub.docker.com/r/nciccbr/mosuite)
+[](https://doi.org/10.5281/zenodo.16371580)
+
+
+Multi-Omics Suite provides a suite of functions to clean, filter, batch-correct,
+normalize, visualize, and perform differential expression analysis. While the
+package is designed for differential [RNA-seq](https://github.com/CCBR/RENEE)
+analysis and multi-omics datasets, it can be used for any data represented in a
+counts table. See the website for more information, documentation, and examples:
+
+
+R package for differential multi-omics analysis
+
+
+
+[](https://github.com/CCBR/MOSuite/actions/workflows/R-CMD-check.yaml)
+[](https://codecov.io/gh/CCBR/MOSuite)
+[](https://github.com/CCBR/MOSuite/actions/workflows/github-code-scanning/codeql)
+[](https://github.com/CCBR/MOSuite/releases/latest)
+[](https://hub.docker.com/r/nciccbr/mosuite)
+[](https://doi.org/10.5281/zenodo.16371580)
+
+
+Multi-Omics Suite provides a suite of functions to clean, filter,
+batch-correct, normalize, visualize, and perform differential expression
+analysis. While the package is designed for differential
+[RNA-seq](https://github.com/CCBR/RENEE) analysis and multi-omics
+datasets, it can be used for any data represented in a counts table. See
+the website for more information, documentation, and examples:
+Log2FC:\", df[[lfc_name]], \n \"
P-value:\", df[[sig_name]]),\n colour = as.character(plot_data$colour),\n fill = as.character(plot_data$colour) # Set fill to the same as colour\n ), \n shape = 21, # Shape that supports both colour and fill\n size = 2, # Size of the points\n stroke = 0.1 # Stroke width\n ) + scale_fill_identity()\n\n# Add interactive hover labels for the gene names\ninteractive_plot <- ggplotly(pxx, tooltip = c(\"text\"))\n\n\n ## showing interactive plot\n grid.newpage()\n print(interactive_plot)\n grid.newpage()\n ## The end of addition\n \n }\n \n df.final <- cbind(df.orig, do.call(cbind, rank))\n return(df.final)\n}\n\n#################################################\n## Global imports and functions included below ##\n#################################################\n\n", + "columns": [ + { + "key": "Column_with_Feature_ID", + "displayName": "Column with Feature ID", + "description": "Column from the input DEG table containing Feature ID (such as Gene Names, Isoform IDs, UniProt IDs, and so on). This is usually the first column (named \"Feature_ID\" or \"Gene\"). Only Text type columns will be allowed.", + "paramGroup": "Basic", + "sourceDataset": "DEG_Table", + "defaultValue": null, + "columnType": "STRING", + "isMulti": null + }, + { + "key": "Significance_Column", + "displayName": "Significance Column", + "description": "Choose an unadjusted or adjusted p-value column from the input DEG table to use as the measure of significance in your Volcano plot. If your DEG analysis contained more than one contrast comparison, you will only be able to select one of these at a time. Make sure you select the same contrast that was selected for the \"Log2 Fold Change Column\" parameter.", + "paramGroup": "Basic", + "sourceDataset": "DEG_Table", + "defaultValue": null, + "columnType": "NUMBER", + "isMulti": true + }, + { + "key": "Log2_Fold_Change_Column", + "displayName": "Log2 Fold Change Column", + "description": "Choose a log2 fold change column from the input DEG table. If your DEG analysis contained more than one contrast comparison, you will only be able to select one of these at a time. Make sure you select the same contrast that was selected for the \"Significance Column\" parameter.", + "paramGroup": "Basic", + "sourceDataset": "DEG_Table", + "defaultValue": null, + "columnType": "NUMBER", + "isMulti": true + } + ], + "condaDependencies": [], + "description": "Implementation of Bioconductor's Enhanced Volcano Plot (v1.6.0, https://bioconductor.org/packages/release/bioc/html/EnhancedVolcano.html). Template written by Matthew Angel and maintained by CCBR. Final Potomac Compatible Version: v52. Final Sugarloaf V1 Version: v55. Latest Sugarloaf V2 Version: v67. [View Documentation](https://nidap.nih.gov/workspace/notepad/view/ri.notepad.main.notepad.8fe3cd6c-db24-4b0a-b717-060cb77ecc5e)", + "externalId": "Volcano_Plot_Enhanced_CCBR_scRNA_seq_Bulk_", + "inputDatasets": [ + { + "key": "DEG_Table", + "displayName": "DEG Table", + "description": "Dataset containing differential expression of genes (DEG) analysis output columns. Usually, this includes columns for gene names, (log) fold changes, (adjusted) p-values, and t-statistics. Other columns may be present.", + "paramGroup": null, + "anchorDataset": false, + "dataType": "R_NATIVE_DATAFRAME", + "tags": [] + } + ], + "vectorLanguage": "R", + "codeLanguage": "R", + "parameters": [ + { + "key": "P_Value_Threshold", + "displayName": "P-Value Threshold", + "description": "", + "paramType": "NUMBER", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": "0.001", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Log2_Fold_Change_Threshold", + "displayName": "Log2 Fold Change Threshold", + "description": "", + "paramType": "NUMBER", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": "1.0", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Choose_Feature_to_Label_By", + "displayName": "Choose Feature to Label By", + "description": "This selection determines how the feature (gene) list is sorted before choosing the top-N features as set by the \"Number of Features to Label\" parameter. Choose either (absolute) fold change, p-value, or t-statistic to label the top features by the selected metric. This also determines which features are labeled in the plot. This option is negated if only using custom labels.", + "paramType": "SELECT", + "paramGroup": "Label", + "paramValues": [ + "p-value", + "fold-change" + ], + "defaultValue": "p-value", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Number_of_Features_to_Label", + "displayName": "Number of Features to Label", + "description": "To minimize clutter on the volcano plot, it is inadvisable to label every feature (gene). You can choose to label any number of features or none. The value of this parameter (N) is used to label the top N features only. See the \"Choose Features To Label By\" parameter for options on how to sort the gene list before labeling the top N features. Will be negated if the option to use only additional labels is selected.", + "paramType": "NUMBER", + "paramGroup": "Label", + "paramValues": null, + "defaultValue": "30", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Label_Only_My_Feature_List", + "displayName": "Label Only My Feature List", + "description": "Select TRUE when you want to label ONLY a specific list of features given in the \"My Feature List\" parameter.", + "paramType": "BOOLEAN", + "paramGroup": "Label", + "paramValues": null, + "defaultValue": "FALSE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Use_Custom_Axis_Label", + "displayName": "Use Custom Axis Label", + "description": "Use text from \"Custom significance label\"?", + "paramType": "BOOLEAN", + "paramGroup": "Title and Axis labels", + "paramValues": null, + "defaultValue": "FALSE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "My_Feature_List", + "displayName": "My Feature List", + "description": "Additional features (genes) to label. If the option to use only custom labels is selected, these will be the only points labeled on the plot. Otherwise, these will be plotted in addition to the other top features. This should be a comma-separated or space-delimited list.", + "paramType": "STRING", + "paramGroup": "Label", + "paramValues": null, + "defaultValue": "", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Top_Genes_Labeled_Only_If_Passing_Thresholds", + "displayName": "Top Genes Labeled Only If Passing Thresholds", + "description": "If TRUE, only genes passing your p-value and logFC thresholds (Basic Parameters) will be labeled on the final plot. If FALSE, genes that do not pass thresholds may be labeled, also. Default is TRUE.", + "paramType": "BOOLEAN", + "paramGroup": "Label", + "paramValues": null, + "defaultValue": "TRUE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Label_Size", + "displayName": "Label Size", + "description": "", + "paramType": "NUMBER", + "paramGroup": "Label", + "paramValues": null, + "defaultValue": "4", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Custom_Significance_Label", + "displayName": "Custom Significance Label", + "description": "This replaces bulky names for the p-value column.", + "paramType": "STRING", + "paramGroup": "Title and Axis labels", + "paramValues": null, + "defaultValue": "p-value", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Custom_Log_Fold_Change_Label", + "displayName": "Custom Log Fold Change Label", + "description": "This replaces bulky column names for the fold-change column.", + "paramType": "STRING", + "paramGroup": "Title and Axis labels", + "paramValues": null, + "defaultValue": "log2FC", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Plot_Title", + "displayName": "Plot Title", + "description": "", + "paramType": "STRING", + "paramGroup": "Title and Axis labels", + "paramValues": null, + "defaultValue": "Volcano Plots", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Y_Limit", + "displayName": "Y-Limit", + "description": "Maximum value for y-axis. Defaults to -log10(min(pval)). Set to 0 for automatic scaling.", + "paramType": "NUMBER", + "paramGroup": "Plot", + "paramValues": null, + "defaultValue": "0", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Custom_X_axis_limits", + "displayName": "Custom X-axis limits", + "description": "Leave empty for automatic scaling, put one number for symmetrical scale (i.e, putting \"5\" would result in a range from \"-5\" to \"5\"), or put two numbers separated by comma for \"asymmetrical\" scale (i.e, putting \"-2,4\" would result in a range from \"-2\" to \"4\")", + "paramType": "STRING", + "paramGroup": "Plot", + "paramValues": null, + "defaultValue": "", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "X_Limit_Padding", + "displayName": "X-Limit Padding", + "description": "Add additional units to x-limit", + "paramType": "NUMBER", + "paramGroup": "Plot", + "paramValues": null, + "defaultValue": "0", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Y_Limit_Padding", + "displayName": "Y-Limit Padding", + "description": "Adds additional units to y-limit.", + "paramType": "NUMBER", + "paramGroup": "Plot", + "paramValues": null, + "defaultValue": "0", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Axis_Label_Size", + "displayName": "Axis Label Size", + "description": "", + "paramType": "NUMBER", + "paramGroup": "Plot", + "paramValues": null, + "defaultValue": "24", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Point_Size", + "displayName": "Point Size", + "description": "", + "paramType": "NUMBER", + "paramGroup": "Plot", + "paramValues": null, + "defaultValue": "2", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Image_Width", + "displayName": "Image Width", + "description": "", + "paramType": "NUMBER", + "paramGroup": "Image", + "paramValues": null, + "defaultValue": "3000", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Image_Height", + "displayName": "Image Height", + "description": "", + "paramType": "NUMBER", + "paramGroup": "Image", + "paramValues": null, + "defaultValue": "3000", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Resolution_DPI_", + "displayName": "Resolution (DPI)", + "description": "", + "paramType": "NUMBER", + "paramGroup": "Image", + "paramValues": null, + "defaultValue": "300", + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "title": "Volcano Plot - Enhanced [CCBR] [scRNA-seq] [Bulk]", + "templateApiVersion": "0.1.0" +} \ No newline at end of file diff --git a/code/MOSuite/inst/extdata/galaxy/0_nidap-1.0/Volcano_Plot_Summary_CCBR_.code-template.json b/code/MOSuite/inst/extdata/galaxy/0_nidap-1.0/Volcano_Plot_Summary_CCBR_.code-template.json new file mode 100644 index 0000000..a4c5a7d --- /dev/null +++ b/code/MOSuite/inst/extdata/galaxy/0_nidap-1.0/Volcano_Plot_Summary_CCBR_.code-template.json @@ -0,0 +1,5126 @@ +{ + "codeTemplate": "Volcano_Summary <- function({{{DEG_Table}}}) {\n # image: {{{Image_Output_Format}}}\n \n stattype<-\"{{{Volcano_P_value_Type}}}\"\n add_deg_columns<-{{{DEG_Columns_to_Keep_in_Output_Table}}}\n image_width = {{{Image_Width}}}\n image_height = {{{Image_Height}}}\n image_resolution = {{{Image_Resolution}}}\n aspect_ratio = {{{Figure_Aspect_Ratio}}}\n\n if ({{{Use_svglite}}} & ((\"{{{Image_Output_Format}}}\" =='svg'))) {\n library(svglite)\n svglite::svglite(\n file=graphicsFile,\n width=image_width,\n height=image_height,\n pointsize=1,\n bg=\"white\",\n )} else if (\"{{{Image_Output_Format}}}\" == 'png') {\n png(\n filename=graphicsFile,\n width=image_width,\n height=image_height,\n units=\"in\",\n pointsize=4,\n bg=\"white\",\n res=image_resolution,\n type=\"cairo\")\n }\n\n suppressMessages(library(ggplot2))\n suppressMessages(library(dplyr))\n suppressMessages(library(ggrepel))\n\n genesmat <- {{{DEG_Table}}}\n value_to_sort_the_output_dataset = \"{{{Choose_Genes_To_Label_By}}}\"\n \n volcols<-colnames(genesmat)\n print(volcols)\n statcols<-volcols[grepl(\"logFC\",volcols)]\n contrasts<-unique(gsub(\"_logFC\",\"\",statcols)) \n \n Plots <- list()\n df_outs <- list()\n for(contrast in contrasts){\n print(paste0(\"Doing contrast: \",contrast))\n lfccol=paste0(contrast,\"_logFC\")\n pvalcol=paste0(contrast,\"_\",stattype)\n tstatcol=paste0(contrast,\"_\",\"tstat\")\n\n print(paste0(\"Fold change column: \",lfccol))\n print(paste0(stattype,\" column: \",pvalcol))\n\n no_genes_to_label <- {{{Number_of_Genes_to_Label}}}\n if (value_to_sort_the_output_dataset==\"fold-change\") {\n genesmat %>% dplyr::arrange(desc(abs(genesmat[,lfccol]))) -> genesmat\n } else if (value_to_sort_the_output_dataset==\"p-value\") {\n genesmat %>% dplyr::arrange(genesmat[,pvalcol]) -> genesmat\n } else if (value_to_sort_the_output_dataset == \"t-statistic\") {\n genesmat %>% dplyr::arrange(desc(abs(genesmat[,tstatcol]))) -> genesmat\n }\n print(paste0(\"Total number of genes included in volcano plot: \", nrow(genesmat)))\n if ({{{Use_Default_Y_Axis_Limit}}}){\n negative_log10_p_values <- -log10(genesmat[,pvalcol])\n ymax <- ceiling(max(negative_log10_p_values[is.finite(negative_log10_p_values)]))\n } else {\n ymax = {{{Y_Axis_Limit}}}\n }\n if ({{{Use_Default_X_Axis_Limit}}}){\n xmax1 = ceiling(max(genesmat[,lfccol]))\n xmax2 = ceiling(max(-genesmat[,lfccol]))\n xmax=max(xmax1,xmax2)\n } else {\n xmax = {{{X_Axis_Limit}}}\n }\n \n\n ## work with a list of genes\nif ({{{Add_My_Gene_List_To_Labels}}}){\n gl <- trimws(unlist(strsplit(c(\"{{{My_Gene_List}}}\"), \",\")), which=c(\"both\"))\n ind <- match(gl, genesmat$Gene) # get the indices of the listed genes\n gene_list_ind <- c(1:no_genes_to_label,ind) # when list provided\n color_gene_label <- c(rep(c(\"{{{Gene_Label_Text_Color}}}\"), no_genes_to_label), rep(c(\"{{{Gene_Label_Text_Color_for_My_Genes}}}\"),length(ind)))\n }else if ({{{Label_Only_My_Gene_List}}}){\n gl <- trimws(unlist(strsplit(c(\"{{{My_Gene_List}}}\"), \",\")), which=c(\"both\")) # unpack the gene list provided by the user and remove white spaces\n ind <- match(gl, genesmat$Gene) # get the indices of the listed genes\n gene_list_ind <- ind # when list provided\n color_gene_label <- rep(c(\"{{{Gene_Label_Text_Color_for_My_Genes}}}\"), length(ind))\n } else {\n if (no_genes_to_label>0) {\n gene_list_ind <- 1:no_genes_to_label # if no list provided label the number of genes given by the user\n color_gene_label <- rep(c(\"{{{Gene_Label_Text_Color}}}\"), no_genes_to_label)\n } else if (no_genes_to_label ==0) {\n gene_list_ind <-0\n }\n } \n\n## special nudge/repel of specific genes\nif ({{{Displace_Gene_Labels}}}){\n gn <- trimws(unlist(strsplit(c(\"{{{Gene_List_Special_Label_Displacement}}}\"), \",\")), which=c(\"both\"))\n ind_gn <- match(gn, genesmat$Gene[gene_list_ind]) # get the indices of the listed genes\n nudge_x_all <- rep(c(0.2), length(genesmat$Gene[gene_list_ind]))\n nudge_y_all <- rep(c(0.2), length(genesmat$Gene[gene_list_ind]))\n nudge_x_all[ind_gn] <- c({{{Special_Label_Displacement_X_Axis_}}})\n nudge_y_all[ind_gn] <- c({{{Special_Label_Displacement_Y_Axis_}}})\n} else {\n nudge_x_all <- {{{Label_Position_Adjustment_X_Axis_}}}\n nudge_y_all <- {{{Label_Position_Adjustment_Y_Axis_}}}\n}\n \n ## flip contrast section\n flipVplot <- {{{Flip_Contrast}}}\n indc <- which(colnames(genesmat) == lfccol) # get the indice of the column that contains the contrast_logFC data\n\n\n if (length(indc)==0){\n print(\"Please rename the logFC column to include the contrast evaluated.\")\n } else{\n old_contrast <- colnames(genesmat)[indc]\n } \n # actually flip contrast\n if (flipVplot){\n # get the indice of the contrast to flip\n indcc <- match(old_contrast,colnames(genesmat)) \n # create flipped contrast label\n splt1 <- strsplit(old_contrast, \"_\") # split by underline symbol to isolate the contrast name\n splt2 <- strsplit(splt1[[1]][1],\"-\") # split the contrast name in the respective components\n flipped_contrast <- paste(splt2[[1]][2], splt2[[1]][1],sep=\"-\") #flip contrast name\n new_contrast_label <- paste(flipped_contrast, c(\"logFC\"), sep = \"_\") \n # rename contrast column to the flipped contrast\n colnames(genesmat)[indcc] <- new_contrast_label\n # flip the contrast data around y-axis\n genesmat[,indcc] <- -genesmat[indcc]\n } else{ new_contrast_label<- old_contrast}\n\n grm<-genesmat[,c(new_contrast_label,pvalcol)]\n grm[,\"neglogpval\"]<- -log10(genesmat[,pvalcol])\n colnames(grm)=c(\"FC\",\"pval\",\"neglogpval\")\n print(grm[gene_list_ind,])\n p <- ggplot(grm,\n aes_string(x = \"FC\", y =\"neglogpval\" ))+ # modified by RAS\n theme_classic() +\n geom_point(\n color='{{{Color_of_Non_Significant_Genes}}}',\n size = {{{Point_Size}}}) +\n geom_vline(xintercept=c(-{{{Log2_Fold_Change_Threshold}}},{{{Log2_Fold_Change_Threshold}}}), color='{{{Color_of_Log_Fold_Change_Threshold_Line}}}', alpha=1.0) + \n geom_hline(yintercept=-log10({{{P_Value_Threshold}}}), color='{{{Color_of_P_Value_Threshold_Line}}}', alpha=1.0) + \n geom_point(\n data = grm[genesmat[,pvalcol] < {{{P_Value_Threshold}}},],\n color = '{{{Color_of_Genes_Meeting_Only_P_Value_Threshold}}}',\n size = {{{Point_Size}}}) +\n geom_point(\n data = grm[genesmat[,pvalcol] < {{{P_Value_Threshold}}} & abs(grm[,\"FC\"])>{{{Log2_Fold_Change_Threshold}}},], \n color = '{{{color_for_genes_meeting_p_value_and_fold_change_thresholds}}}',\n size = {{{Point_Size}}}) +\n geom_text_repel(\n data = grm[gene_list_ind,], \n label = genesmat${{{Gene_Names_Column}}}[gene_list_ind], \n color = color_gene_label,\n fontface = {{{Label_Font_Type}}},\n nudge_x = nudge_x_all,\n nudge_y = nudge_y_all,\n size = {{{Label_Font_Size}}},\n segment.size = {{{Line_Segment_Thickness}}}) +\n xlim(-xmax,xmax) +\n ylim(0,ymax) + xlab(new_contrast_label) + ylab(pvalcol)\n\n if (aspect_ratio > 0){\n p <- p + coord_fixed(ratio=aspect_ratio)\n }\n \n #print(p)\n Plots[[contrast]]=p\n print(head(genesmat[,pvalcol] ))\n filtered_genes = genesmat${{{Gene_Names_Column}}}[genesmat[,pvalcol] < {{{P_Value_Threshold}}} & abs(grm[,\"FC\"])>{{{Log2_Fold_Change_Threshold}}}]\n #print(filtered_genes)\n repeated_column = rep(contrast, length(filtered_genes))\n ## If param empty upon template upgrade, fill it with default value.\n if (length(add_deg_columns) == 0) {\n add_deg_columns <- c(\"FC\",\"logFC\",\"tstat\",\"pval\",\"adjpval\")\n }\n ## Get columns for output table.\n if (add_deg_columns == \"none\") {\n new_df <- data.frame(filtered_genes, repeated_column)\n names(new_df) <- c(\"Gene\", \"Contrast\")\n } else {\n add_deg_columns = setdiff(add_deg_columns, \"none\")\n out_columns = paste(contrast, add_deg_columns, sep=\"_\")\n deg = genesmat[,c(\"{{{Gene_Names_Column}}}\", out_columns)]\n names(deg)[1] = \"Gene\"\n new_df <- data.frame(filtered_genes, repeated_column) %>% dplyr::left_join(deg, by=c(\"filtered_genes\"=\"Gene\"))\n names(new_df) <- c(\"Gene\", \"Contrast\", add_deg_columns)\n }\n\n df_out1 <- new_df\n df_outs[[contrast]]=df_out1\n }\n\n Use_default_grid_layout = {{{Use_Default_Grid_Layout}}}\n require(gridExtra)\n nplots=length(Plots)\n if (Use_default_grid_layout) {\n nrows=ceiling(nplots/ceiling(sqrt(nplots)))\n } else {\n nrows = {{{Number_of_Rows_in_Grid_Layout}}}\n }\n\n do.call(\"grid.arrange\", c(Plots, nrow=nrows))\n print(\"done plotting\")\n\n df_out <- unique(do.call(\"rbind\", df_outs))\n print(head(df_out))\n print(colnames(df_out))\n return(df_out)\n}\n\n \n", + "columns": [ + { + "key": "Gene_Names_Column", + "displayName": "Gene Names Column", + "description": "The column from your input DEG table containing the gene names. This is usually the first column. Only columns of Text type from your DEG table will be available to select for this parameter.", + "paramGroup": "Basic", + "sourceDataset": "DEG_Table", + "defaultValue": null, + "columnType": "STRING", + "isMulti": null + } + ], + "condaDependencies": [], + "description": "Produces one volcano plot for each tested contrast in the input DEG table.\n\nIt can be sorted by either fold change, t-statistic, or p-value. The returned dataset includes one row for each significant gene in each contrast, and contains columns from the DEG analysis of that contrast as well as columns useful to the Venn diagram template downstream.", + "externalId": "Volcano_Plot_Summary_CCBR_", + "inputDatasets": [ + { + "key": "DEG_Table", + "displayName": "DEG Table", + "description": "Dataset containing differential expression of genes (DEG) analysis output columns. Usually, this includes columns for gene names, (log) fold changes, (adjusted) p-values, and t-statistics. Other columns may also be present.", + "paramGroup": "Basic", + "anchorDataset": false, + "dataType": "R_NATIVE_DATAFRAME", + "tags": [] + } + ], + "vectorLanguage": "R", + "codeLanguage": "R", + "parameters": [ + { + "key": "Volcano_P_value_Type", + "displayName": "Volcano P-value Type", + "description": "Choose whether to use unadjusted or adjusted p-values in the resulting volcano plots.", + "paramType": "SELECT", + "paramGroup": "Basic", + "paramValues": [ + "pval", + "adjpval" + ], + "defaultValue": "pval", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "P_Value_Threshold", + "displayName": "P-Value Threshold", + "description": "Generates a horizontal blue line at -log10 of this value on the y-axis of the volcano plot. Genes located above this threshold are considered significantly differentially expressed.", + "paramType": "NUMBER", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": "0.001", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Log2_Fold_Change_Threshold", + "displayName": "Log2 Fold Change Threshold", + "description": "Generates two vertical red lines at +/- this value on the x-axis of the volcano plot. A value of 1 entered here will draw lines at a log2 fold change values of -1 and 1. This corresponds to unlogged fold changes of 2 and 1/2, respectively.", + "paramType": "NUMBER", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": "1", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Choose_Genes_To_Label_By", + "displayName": "Choose Genes To Label By", + "description": "This selection determines how the gene list is sorted before choosing the top-N genes as set by the \"Number of Genes to Label\" parameter. Choose either (absolute) fold change, p-value, or t-statistic to label the top genes by the selected metric.", + "paramType": "SELECT", + "paramGroup": "Gene Name Label", + "paramValues": [ + "fold-change", + "p-value", + "t-statistic" + ], + "defaultValue": "t-statistic", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Number_of_Genes_to_Label", + "displayName": "Number of Genes to Label", + "description": "To minimize clutter on the volcano plot, it is inadvisable to label every gene. You can choose to label any number of genes or none. The value of this parameter (N) is used to label the top N genes only. See the \"Choose Genes To Label By\" parameter for options on how to sort the gene list before labeling the top N genes.", + "paramType": "NUMBER", + "paramGroup": "Gene Name Label", + "paramValues": null, + "defaultValue": "30", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Add_My_Gene_List_To_Labels", + "displayName": "Add My Gene List To Labels", + "description": "Set TRUE when you want to label a specific set of genes in the \"My Gene List\" parameter\" IN ADDITION to the number of genes you set in the \"Number of Genes to Label\" parameter.", + "paramType": "BOOLEAN", + "paramGroup": "Gene Name Label", + "paramValues": null, + "defaultValue": "FALSE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Label_Only_My_Gene_List", + "displayName": "Label Only My Gene List", + "description": "Select TRUE when you want to label ONLY a specific list of genes given in the \"My Gene List\" parameter.", + "paramType": "BOOLEAN", + "paramGroup": "Gene Name Label", + "paramValues": null, + "defaultValue": "FALSE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "My_Gene_List", + "displayName": "My Gene List", + "description": "Provide a list of genes (comma separated) to be labeled on the volcano plot. You must toggle one of the following ON to see these labels: \"Add My Gene List To Labels\" or \"Label Only My Gene List\".", + "paramType": "STRING", + "paramGroup": "Gene Name Label", + "paramValues": null, + "defaultValue": "Provide list of genes-comma separated", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Gene_Label_Text_Color", + "displayName": "Gene Label Text Color", + "description": "Set the color for the text used to add gene name labels to points.", + "paramType": "SELECT", + "paramGroup": "Gene Name Label", + "paramValues": [ + "white", + "aliceblue", + "antiquewhite", + "antiquewhite1", + "antiquewhite2", + "antiquewhite3", + "antiquewhite4", + "aquamarine", + "aquamarine1", + "aquamarine2", + "aquamarine3", + "aquamarine4", + "azure", + "azure1", + "azure2", + "azure3", + "azure4", + "beige", + "bisque", + "bisque1", + "bisque2", + "bisque3", + "bisque4", + "black", + "blanchedalmond", + "blue", + "blue1", + "blue2", + "blue3", + "blue4", + "blueviolet", + "brown", + "brown1", + "brown2", + "brown3", + "brown4", + "burlywood", + "burlywood1", + "burlywood2", + "burlywood3", + "burlywood4", + "cadetblue", + "cadetblue1", + "cadetblue2", + "cadetblue3", + "cadetblue4", + "chartreuse", + "chartreuse1", + "chartreuse2", + "chartreuse3", + "chartreuse4", + "chocolate", + "chocolate1", + "chocolate2", + "chocolate3", + "chocolate4", + "coral", + "coral1", + "coral2", + "coral3", + "coral4", + "cornflowerblue", + "cornsilk", + "cornsilk1", + "cornsilk2", + "cornsilk3", + "cornsilk4", + "cyan", + "cyan1", + "cyan2", + "cyan3", + "cyan4", + "darkblue", + "darkcyan", + "darkgoldenrod", + "darkgoldenrod1", + "darkgoldenrod2", + "darkgoldenrod3", + "darkgoldenrod4", + "darkgray", + "darkgreen", + "darkgrey", + "darkkhaki", + "darkmagenta", + "darkolivegreen", + "darkolivegreen1", + "darkolivegreen2", + "darkolivegreen3", + "darkolivegreen4", + "darkorange", + "darkorange1", + "darkorange2", + "darkorange3", + "darkorange4", + "darkorchid", + "darkorchid1", + "darkorchid2", + "darkorchid3", + "darkorchid4", + "darkred", + "darksalmon", + "darkseagreen", + "darkseagreen1", + "darkseagreen2", + "darkseagreen3", + "darkseagreen4", + "darkslateblue", + "darkslategray", + "darkslategray1", + "darkslategray2", + "darkslategray3", + "darkslategray4", + "darkslategrey", + "darkturquoise", + "darkviolet", + "deeppink", + "deeppink1", + "deeppink2", + "deeppink3", + "deeppink4", + "deepskyblue", + "deepskyblue1", + "deepskyblue2", + "deepskyblue3", + "deepskyblue4", + "dimgray", + "dimgrey", + "dodgerblue", + "dodgerblue1", + "dodgerblue2", + "dodgerblue3", + "dodgerblue4", + "firebrick", + "firebrick1", + "firebrick2", + "firebrick3", + "firebrick4", + "floralwhite", + "forestgreen", + "gainsboro", + "ghostwhite", + "gold", + "gold1", + "gold2", + "gold3", + "gold4", + "goldenrod", + "goldenrod1", + "goldenrod2", + "goldenrod3", + "goldenrod4", + "gray", + "gray0", + "gray1", + "gray2", + "gray3", + "gray4", + "gray5", + "gray6", + "gray7", + "gray8", + "gray9", + "gray10", + "gray11", + "gray12", + "gray13", + "gray14", + "gray15", + "gray16", + "gray17", + "gray18", + "gray19", + "gray20", + "gray21", + "gray22", + "gray23", + "gray24", + "gray25", + "gray26", + "gray27", + "gray28", + "gray29", + "gray30", + "gray31", + "gray32", + "gray33", + "gray34", + "gray35", + "gray36", + "gray37", + "gray38", + "gray39", + "gray40", + "gray41", + "gray42", + "gray43", + "gray44", + "gray45", + "gray46", + "gray47", + "gray48", + "gray49", + "gray50", + "gray51", + "gray52", + "gray53", + "gray54", + "gray55", + "gray56", + "gray57", + "gray58", + "gray59", + "gray60", + "gray61", + "gray62", + "gray63", + "gray64", + "gray65", + "gray66", + "gray67", + "gray68", + "gray69", + "gray70", + "gray71", + "gray72", + "gray73", + "gray74", + "gray75", + "gray76", + "gray77", + "gray78", + "gray79", + "gray80", + "gray81", + "gray82", + "gray83", + "gray84", + "gray85", + "gray86", + "gray87", + "gray88", + "gray89", + "gray90", + "gray91", + "gray92", + "gray93", + "gray94", + "gray95", + "gray96", + "gray97", + "gray98", + "gray99", + "gray100", + "green", + "green1", + "green2", + "green3", + "green4", + "greenyellow", + "grey", + "grey0", + "grey1", + "grey2", + "grey3", + "grey4", + "grey5", + "grey6", + "grey7", + "grey8", + "grey9", + "grey10", + "grey11", + "grey12", + "grey13", + "grey14", + "grey15", + "grey16", + "grey17", + "grey18", + "grey19", + "grey20", + "grey21", + "grey22", + "grey23", + "grey24", + "grey25", + "grey26", + "grey27", + "grey28", + "grey29", + "grey30", + "grey31", + "grey32", + "grey33", + "grey34", + "grey35", + "grey36", + "grey37", + "grey38", + "grey39", + "grey40", + "grey41", + "grey42", + "grey43", + "grey44", + "grey45", + "grey46", + "grey47", + "grey48", + "grey49", + "grey50", + "grey51", + "grey52", + "grey53", + "grey54", + "grey55", + "grey56", + "grey57", + "grey58", + "grey59", + "grey60", + "grey61", + "grey62", + "grey63", + "grey64", + "grey65", + "grey66", + "grey67", + "grey68", + "grey69", + "grey70", + "grey71", + "grey72", + "grey73", + "grey74", + "grey75", + "grey76", + "grey77", + "grey78", + "grey79", + "grey80", + "grey81", + "grey82", + "grey83", + "grey84", + "grey85", + "grey86", + "grey87", + "grey88", + "grey89", + "grey90", + "grey91", + "grey92", + "grey93", + "grey94", + "grey95", + "grey96", + "grey97", + "grey98", + "grey99", + "grey100", + "honeydew", + "honeydew1", + "honeydew2", + "honeydew3", + "honeydew4", + "hotpink", + "hotpink1", + "hotpink2", + "hotpink3", + "hotpink4", + "indianred", + "indianred1", + "indianred2", + "indianred3", + "indianred4", + "ivory", + "ivory1", + "ivory2", + "ivory3", + "ivory4", + "khaki", + "khaki1", + "khaki2", + "khaki3", + "khaki4", + "lavender", + "lavenderblush", + "lavenderblush1", + "lavenderblush2", + "lavenderblush3", + "lavenderblush4", + "lawngreen", + "lemonchiffon", + "lemonchiffon1", + "lemonchiffon2", + "lemonchiffon3", + "lemonchiffon4", + "lightblue", + "lightblue1", + "lightblue2", + "lightblue3", + "lightblue4", + "lightcoral", + "lightcyan", + "lightcyan1", + "lightcyan2", + "lightcyan3", + "lightcyan4", + "lightgoldenrod", + "lightgoldenrod1", + "lightgoldenrod2", + "lightgoldenrod3", + "lightgoldenrod4", + "lightgoldenrodyellow", + "lightgray", + "lightgreen", + "lightgrey", + "lightpink", + "lightpink1", + "lightpink2", + "lightpink3", + "lightpink4", + "lightsalmon", + "lightsalmon1", + "lightsalmon2", + "lightsalmon3", + "lightsalmon4", + "lightseagreen", + "lightskyblue", + "lightskyblue1", + "lightskyblue2", + "lightskyblue3", + "lightskyblue4", + "lightslateblue", + "lightslategray", + "lightslategrey", + "lightsteelblue", + "lightsteelblue1", + "lightsteelblue2", + "lightsteelblue3", + "lightsteelblue4", + "lightyellow", + "lightyellow1", + "lightyellow2", + "lightyellow3", + "lightyellow4", + "limegreen", + "linen", + "magenta", + "magenta1", + "magenta2", + "magenta3", + "magenta4", + "maroon", + "maroon1", + "maroon2", + "maroon3", + "maroon4", + "mediumaquamarine", + "mediumblue", + "mediumorchid", + "mediumorchid1", + "mediumorchid2", + "mediumorchid3", + "mediumorchid4", + "mediumpurple", + "mediumpurple1", + "mediumpurple2", + "mediumpurple3", + "mediumpurple4", + "mediumseagreen", + "mediumslateblue", + "mediumspringgreen", + "mediumturquoise", + "mediumvioletred", + "midnightblue", + "mintcream", + "mistyrose", + "mistyrose1", + "mistyrose2", + "mistyrose3", + "mistyrose4", + "moccasin", + "navajowhite", + "navajowhite1", + "navajowhite2", + "navajowhite3", + "navajowhite4", + "navy", + "navyblue", + "oldlace", + "olivedrab", + "olivedrab1", + "olivedrab2", + "olivedrab3", + "olivedrab4", + "orange", + "orange1", + "orange2", + "orange3", + "orange4", + "orangered", + "orangered1", + "orangered2", + "orangered3", + "orangered4", + "orchid", + "orchid1", + "orchid2", + "orchid3", + "orchid4", + "palegoldenrod", + "palegreen", + "palegreen1", + "palegreen2", + "palegreen3", + "palegreen4", + "paleturquoise", + "paleturquoise1", + "paleturquoise2", + "paleturquoise3", + "paleturquoise4", + "palevioletred", + "palevioletred1", + "palevioletred2", + "palevioletred3", + "palevioletred4", + "papayawhip", + "peachpuff", + "peachpuff1", + "peachpuff2", + "peachpuff3", + "peachpuff4", + "peru", + "pink", + "pink1", + "pink2", + "pink3", + "pink4", + "plum", + "plum1", + "plum2", + "plum3", + "plum4", + "powderblue", + "purple", + "purple1", + "purple2", + "purple3", + "purple4", + "red", + "red1", + "red2", + "red3", + "red4", + "rosybrown", + "rosybrown1", + "rosybrown2", + "rosybrown3", + "rosybrown4", + "royalblue", + "royalblue1", + "royalblue2", + "royalblue3", + "royalblue4", + "saddlebrown", + "salmon", + "salmon1", + "salmon2", + "salmon3", + "salmon4", + "sandybrown", + "seagreen", + "seagreen1", + "seagreen2", + "seagreen3", + "seagreen4", + "seashell", + "seashell1", + "seashell2", + "seashell3", + "seashell4", + "sienna", + "sienna1", + "sienna2", + "sienna3", + "sienna4", + "skyblue", + "skyblue1", + "skyblue2", + "skyblue3", + "skyblue4", + "slateblue", + "slateblue1", + "slateblue2", + "slateblue3", + "slateblue4", + "slategray", + "slategray1", + "slategray2", + "slategray3", + "slategray4", + "slategrey", + "snow", + "snow1", + "snow2", + "snow3", + "snow4", + "springgreen", + "springgreen1", + "springgreen2", + "springgreen3", + "springgreen4", + "steelblue", + "steelblue1", + "steelblue2", + "steelblue3", + "steelblue4", + "tan", + "tan1", + "tan2", + "tan3", + "tan4", + "thistle", + "thistle1", + "thistle2", + "thistle3", + "thistle4", + "tomato", + "tomato1", + "tomato2", + "tomato3", + "tomato4", + "turquoise", + "turquoise1", + "turquoise2", + "turquoise3", + "turquoise4", + "violet", + "violetred", + "violetred1", + "violetred2", + "violetred3", + "violetred4", + "wheat", + "wheat1", + "wheat2", + "wheat3", + "wheat4", + "whitesmoke", + "yellow", + "yellow1", + "yellow2", + "yellow3", + "yellow4", + "yellowgreen" + ], + "defaultValue": "black", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Gene_Label_Text_Color_for_My_Genes", + "displayName": "Gene Label Text Color for My Genes", + "description": "Set the color for the specific list of genes provided in the \"Gene List\" parameter.", + "paramType": "SELECT", + "paramGroup": "Gene Name Label", + "paramValues": [ + "white", + "aliceblue", + "antiquewhite", + "antiquewhite1", + "antiquewhite2", + "antiquewhite3", + "antiquewhite4", + "aquamarine", + "aquamarine1", + "aquamarine2", + "aquamarine3", + "aquamarine4", + "azure", + "azure1", + "azure2", + "azure3", + "azure4", + "beige", + "bisque", + "bisque1", + "bisque2", + "bisque3", + "bisque4", + "black", + "blanchedalmond", + "blue", + "blue1", + "blue2", + "blue3", + "blue4", + "blueviolet", + "brown", + "brown1", + "brown2", + "brown3", + "brown4", + "burlywood", + "burlywood1", + "burlywood2", + "burlywood3", + "burlywood4", + "cadetblue", + "cadetblue1", + "cadetblue2", + "cadetblue3", + "cadetblue4", + "chartreuse", + "chartreuse1", + "chartreuse2", + "chartreuse3", + "chartreuse4", + "chocolate", + "chocolate1", + "chocolate2", + "chocolate3", + "chocolate4", + "coral", + "coral1", + "coral2", + "coral3", + "coral4", + "cornflowerblue", + "cornsilk", + "cornsilk1", + "cornsilk2", + "cornsilk3", + "cornsilk4", + "cyan", + "cyan1", + "cyan2", + "cyan3", + "cyan4", + "darkblue", + "darkcyan", + "darkgoldenrod", + "darkgoldenrod1", + "darkgoldenrod2", + "darkgoldenrod3", + "darkgoldenrod4", + "darkgray", + "darkgreen", + "darkgrey", + "darkkhaki", + "darkmagenta", + "darkolivegreen", + "darkolivegreen1", + "darkolivegreen2", + "darkolivegreen3", + "darkolivegreen4", + "darkorange", + "darkorange1", + "darkorange2", + "darkorange3", + "darkorange4", + "darkorchid", + "darkorchid1", + "darkorchid2", + "darkorchid3", + "darkorchid4", + "darkred", + "darksalmon", + "darkseagreen", + "darkseagreen1", + "darkseagreen2", + "darkseagreen3", + "darkseagreen4", + "darkslateblue", + "darkslategray", + "darkslategray1", + "darkslategray2", + "darkslategray3", + "darkslategray4", + "darkslategrey", + "darkturquoise", + "darkviolet", + "deeppink", + "deeppink1", + "deeppink2", + "deeppink3", + "deeppink4", + "deepskyblue", + "deepskyblue1", + "deepskyblue2", + "deepskyblue3", + "deepskyblue4", + "dimgray", + "dimgrey", + "dodgerblue", + "dodgerblue1", + "dodgerblue2", + "dodgerblue3", + "dodgerblue4", + "firebrick", + "firebrick1", + "firebrick2", + "firebrick3", + "firebrick4", + "floralwhite", + "forestgreen", + "gainsboro", + "ghostwhite", + "gold", + "gold1", + "gold2", + "gold3", + "gold4", + "goldenrod", + "goldenrod1", + "goldenrod2", + "goldenrod3", + "goldenrod4", + "gray", + "gray0", + "gray1", + "gray2", + "gray3", + "gray4", + "gray5", + "gray6", + "gray7", + "gray8", + "gray9", + "gray10", + "gray11", + "gray12", + "gray13", + "gray14", + "gray15", + "gray16", + "gray17", + "gray18", + "gray19", + "gray20", + "gray21", + "gray22", + "gray23", + "gray24", + "gray25", + "gray26", + "gray27", + "gray28", + "gray29", + "gray30", + "gray31", + "gray32", + "gray33", + "gray34", + "gray35", + "gray36", + "gray37", + "gray38", + "gray39", + "gray40", + "gray41", + "gray42", + "gray43", + "gray44", + "gray45", + "gray46", + "gray47", + "gray48", + "gray49", + "gray50", + "gray51", + "gray52", + "gray53", + "gray54", + "gray55", + "gray56", + "gray57", + "gray58", + "gray59", + "gray60", + "gray61", + "gray62", + "gray63", + "gray64", + "gray65", + "gray66", + "gray67", + "gray68", + "gray69", + "gray70", + "gray71", + "gray72", + "gray73", + "gray74", + "gray75", + "gray76", + "gray77", + "gray78", + "gray79", + "gray80", + "gray81", + "gray82", + "gray83", + "gray84", + "gray85", + "gray86", + "gray87", + "gray88", + "gray89", + "gray90", + "gray91", + "gray92", + "gray93", + "gray94", + "gray95", + "gray96", + "gray97", + "gray98", + "gray99", + "gray100", + "green", + "green1", + "green2", + "green3", + "green4", + "greenyellow", + "grey", + "grey0", + "grey1", + "grey2", + "grey3", + "grey4", + "grey5", + "grey6", + "grey7", + "grey8", + "grey9", + "grey10", + "grey11", + "grey12", + "grey13", + "grey14", + "grey15", + "grey16", + "grey17", + "grey18", + "grey19", + "grey20", + "grey21", + "grey22", + "grey23", + "grey24", + "grey25", + "grey26", + "grey27", + "grey28", + "grey29", + "grey30", + "grey31", + "grey32", + "grey33", + "grey34", + "grey35", + "grey36", + "grey37", + "grey38", + "grey39", + "grey40", + "grey41", + "grey42", + "grey43", + "grey44", + "grey45", + "grey46", + "grey47", + "grey48", + "grey49", + "grey50", + "grey51", + "grey52", + "grey53", + "grey54", + "grey55", + "grey56", + "grey57", + "grey58", + "grey59", + "grey60", + "grey61", + "grey62", + "grey63", + "grey64", + "grey65", + "grey66", + "grey67", + "grey68", + "grey69", + "grey70", + "grey71", + "grey72", + "grey73", + "grey74", + "grey75", + "grey76", + "grey77", + "grey78", + "grey79", + "grey80", + "grey81", + "grey82", + "grey83", + "grey84", + "grey85", + "grey86", + "grey87", + "grey88", + "grey89", + "grey90", + "grey91", + "grey92", + "grey93", + "grey94", + "grey95", + "grey96", + "grey97", + "grey98", + "grey99", + "grey100", + "honeydew", + "honeydew1", + "honeydew2", + "honeydew3", + "honeydew4", + "hotpink", + "hotpink1", + "hotpink2", + "hotpink3", + "hotpink4", + "indianred", + "indianred1", + "indianred2", + "indianred3", + "indianred4", + "ivory", + "ivory1", + "ivory2", + "ivory3", + "ivory4", + "khaki", + "khaki1", + "khaki2", + "khaki3", + "khaki4", + "lavender", + "lavenderblush", + "lavenderblush1", + "lavenderblush2", + "lavenderblush3", + "lavenderblush4", + "lawngreen", + "lemonchiffon", + "lemonchiffon1", + "lemonchiffon2", + "lemonchiffon3", + "lemonchiffon4", + "lightblue", + "lightblue1", + "lightblue2", + "lightblue3", + "lightblue4", + "lightcoral", + "lightcyan", + "lightcyan1", + "lightcyan2", + "lightcyan3", + "lightcyan4", + "lightgoldenrod", + "lightgoldenrod1", + "lightgoldenrod2", + "lightgoldenrod3", + "lightgoldenrod4", + "lightgoldenrodyellow", + "lightgray", + "lightgreen", + "lightgrey", + "lightpink", + "lightpink1", + "lightpink2", + "lightpink3", + "lightpink4", + "lightsalmon", + "lightsalmon1", + "lightsalmon2", + "lightsalmon3", + "lightsalmon4", + "lightseagreen", + "lightskyblue", + "lightskyblue1", + "lightskyblue2", + "lightskyblue3", + "lightskyblue4", + "lightslateblue", + "lightslategray", + "lightslategrey", + "lightsteelblue", + "lightsteelblue1", + "lightsteelblue2", + "lightsteelblue3", + "lightsteelblue4", + "lightyellow", + "lightyellow1", + "lightyellow2", + "lightyellow3", + "lightyellow4", + "limegreen", + "linen", + "magenta", + "magenta1", + "magenta2", + "magenta3", + "magenta4", + "maroon", + "maroon1", + "maroon2", + "maroon3", + "maroon4", + "mediumaquamarine", + "mediumblue", + "mediumorchid", + "mediumorchid1", + "mediumorchid2", + "mediumorchid3", + "mediumorchid4", + "mediumpurple", + "mediumpurple1", + "mediumpurple2", + "mediumpurple3", + "mediumpurple4", + "mediumseagreen", + "mediumslateblue", + "mediumspringgreen", + "mediumturquoise", + "mediumvioletred", + "midnightblue", + "mintcream", + "mistyrose", + "mistyrose1", + "mistyrose2", + "mistyrose3", + "mistyrose4", + "moccasin", + "navajowhite", + "navajowhite1", + "navajowhite2", + "navajowhite3", + "navajowhite4", + "navy", + "navyblue", + "oldlace", + "olivedrab", + "olivedrab1", + "olivedrab2", + "olivedrab3", + "olivedrab4", + "orange", + "orange1", + "orange2", + "orange3", + "orange4", + "orangered", + "orangered1", + "orangered2", + "orangered3", + "orangered4", + "orchid", + "orchid1", + "orchid2", + "orchid3", + "orchid4", + "palegoldenrod", + "palegreen", + "palegreen1", + "palegreen2", + "palegreen3", + "palegreen4", + "paleturquoise", + "paleturquoise1", + "paleturquoise2", + "paleturquoise3", + "paleturquoise4", + "palevioletred", + "palevioletred1", + "palevioletred2", + "palevioletred3", + "palevioletred4", + "papayawhip", + "peachpuff", + "peachpuff1", + "peachpuff2", + "peachpuff3", + "peachpuff4", + "peru", + "pink", + "pink1", + "pink2", + "pink3", + "pink4", + "plum", + "plum1", + "plum2", + "plum3", + "plum4", + "powderblue", + "purple", + "purple1", + "purple2", + "purple3", + "purple4", + "red", + "red1", + "red2", + "red3", + "red4", + "rosybrown", + "rosybrown1", + "rosybrown2", + "rosybrown3", + "rosybrown4", + "royalblue", + "royalblue1", + "royalblue2", + "royalblue3", + "royalblue4", + "saddlebrown", + "salmon", + "salmon1", + "salmon2", + "salmon3", + "salmon4", + "sandybrown", + "seagreen", + "seagreen1", + "seagreen2", + "seagreen3", + "seagreen4", + "seashell", + "seashell1", + "seashell2", + "seashell3", + "seashell4", + "sienna", + "sienna1", + "sienna2", + "sienna3", + "sienna4", + "skyblue", + "skyblue1", + "skyblue2", + "skyblue3", + "skyblue4", + "slateblue", + "slateblue1", + "slateblue2", + "slateblue3", + "slateblue4", + "slategray", + "slategray1", + "slategray2", + "slategray3", + "slategray4", + "slategrey", + "snow", + "snow1", + "snow2", + "snow3", + "snow4", + "springgreen", + "springgreen1", + "springgreen2", + "springgreen3", + "springgreen4", + "steelblue", + "steelblue1", + "steelblue2", + "steelblue3", + "steelblue4", + "tan", + "tan1", + "tan2", + "tan3", + "tan4", + "thistle", + "thistle1", + "thistle2", + "thistle3", + "thistle4", + "tomato", + "tomato1", + "tomato2", + "tomato3", + "tomato4", + "turquoise", + "turquoise1", + "turquoise2", + "turquoise3", + "turquoise4", + "violet", + "violetred", + "violetred1", + "violetred2", + "violetred3", + "violetred4", + "wheat", + "wheat1", + "wheat2", + "wheat3", + "wheat4", + "whitesmoke", + "yellow", + "yellow1", + "yellow2", + "yellow3", + "yellow4", + "yellowgreen" + ], + "defaultValue": "green3", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Label_Position_Adjustment_X_Axis_", + "displayName": "Label Position Adjustment (X-Axis)", + "description": "", + "paramType": "NUMBER", + "paramGroup": "Gene Name Label", + "paramValues": null, + "defaultValue": "0.2", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Label_Position_Adjustment_Y_Axis_", + "displayName": "Label Position Adjustment (Y-Axis)", + "description": "", + "paramType": "NUMBER", + "paramGroup": "Gene Name Label", + "paramValues": null, + "defaultValue": "0.2", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Line_Segment_Thickness", + "displayName": "Line Segment Thickness", + "description": "Thickness of the line connecting the point and it's gene label", + "paramType": "NUMBER", + "paramGroup": "Gene Name Label", + "paramValues": null, + "defaultValue": "0.5", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Label_Font_Size", + "displayName": "Label Font Size", + "description": "Font size for sample labels. Set to 0 to remove labels.", + "paramType": "STRING", + "paramGroup": "Gene Name Label", + "paramValues": null, + "defaultValue": "4", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Label_Font_Type", + "displayName": "Label Font Type", + "description": "Select the font type for the gene labels displayed in the volcano plot. The options are: 1-regular, 2-bold, 3-italic, 4-bold.italic, 5-greek alphabet.", + "paramType": "NUMBER", + "paramGroup": "Gene Name Label", + "paramValues": null, + "defaultValue": "1", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Displace_Gene_Labels", + "displayName": "Displace Gene Labels", + "description": "Set TRUE if you want to displace the gene label for a specific set of genes. Make sure to use custom x- and y- limits and give sufficient space for displacement; otherwise other labels than the desired ones will appear displaced.", + "paramType": "BOOLEAN", + "paramGroup": "Gene Name Label", + "paramValues": null, + "defaultValue": "FALSE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Gene_List_Special_Label_Displacement", + "displayName": "Gene List Special Label Displacement", + "description": "Provide a list of genes (comma separated) for which you want special displacement of the gene label.", + "paramType": "STRING", + "paramGroup": "Gene Name Label", + "paramValues": null, + "defaultValue": "Provide list of genes-comma separated", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Special_Label_Displacement_X_Axis_", + "displayName": "Special Label Displacement (X-Axis)", + "description": "Choose a number to set the nudge/displacement of the gene label in the x-direction.", + "paramType": "NUMBER", + "paramGroup": "Gene Name Label", + "paramValues": null, + "defaultValue": "2", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Special_Label_Displacement_Y_Axis_", + "displayName": "Special Label Displacement (Y-Axis)", + "description": "Choose a number (comma separated) to set the nudge/displacement of the gene label in the x-direction.", + "paramType": "NUMBER", + "paramGroup": "Gene Name Label", + "paramValues": null, + "defaultValue": "2", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Color_of_P_Value_Threshold_Line", + "displayName": "Color of P-Value Threshold Line", + "description": "The color of the horizontal p-value threshold line", + "paramType": "SELECT", + "paramGroup": "Plot", + "paramValues": [ + "white", + "aliceblue", + "antiquewhite", + "antiquewhite1", + "antiquewhite2", + "antiquewhite3", + "antiquewhite4", + "aquamarine", + "aquamarine1", + "aquamarine2", + "aquamarine3", + "aquamarine4", + "azure", + "azure1", + "azure2", + "azure3", + "azure4", + "beige", + "bisque", + "bisque1", + "bisque2", + "bisque3", + "bisque4", + "black", + "blanchedalmond", + "blue", + "blue1", + "blue2", + "blue3", + "blue4", + "blueviolet", + "brown", + "brown1", + "brown2", + "brown3", + "brown4", + "burlywood", + "burlywood1", + "burlywood2", + "burlywood3", + "burlywood4", + "cadetblue", + "cadetblue1", + "cadetblue2", + "cadetblue3", + "cadetblue4", + "chartreuse", + "chartreuse1", + "chartreuse2", + "chartreuse3", + "chartreuse4", + "chocolate", + "chocolate1", + "chocolate2", + "chocolate3", + "chocolate4", + "coral", + "coral1", + "coral2", + "coral3", + "coral4", + "cornflowerblue", + "cornsilk", + "cornsilk1", + "cornsilk2", + "cornsilk3", + "cornsilk4", + "cyan", + "cyan1", + "cyan2", + "cyan3", + "cyan4", + "darkblue", + "darkcyan", + "darkgoldenrod", + "darkgoldenrod1", + "darkgoldenrod2", + "darkgoldenrod3", + "darkgoldenrod4", + "darkgray", + "darkgreen", + "darkgrey", + "darkkhaki", + "darkmagenta", + "darkolivegreen", + "darkolivegreen1", + "darkolivegreen2", + "darkolivegreen3", + "darkolivegreen4", + "darkorange", + "darkorange1", + "darkorange2", + "darkorange3", + "darkorange4", + "darkorchid", + "darkorchid1", + "darkorchid2", + "darkorchid3", + "darkorchid4", + "darkred", + "darksalmon", + "darkseagreen", + "darkseagreen1", + "darkseagreen2", + "darkseagreen3", + "darkseagreen4", + "darkslateblue", + "darkslategray", + "darkslategray1", + "darkslategray2", + "darkslategray3", + "darkslategray4", + "darkslategrey", + "darkturquoise", + "darkviolet", + "deeppink", + "deeppink1", + "deeppink2", + "deeppink3", + "deeppink4", + "deepskyblue", + "deepskyblue1", + "deepskyblue2", + "deepskyblue3", + "deepskyblue4", + "dimgray", + "dimgrey", + "dodgerblue", + "dodgerblue1", + "dodgerblue2", + "dodgerblue3", + "dodgerblue4", + "firebrick", + "firebrick1", + "firebrick2", + "firebrick3", + "firebrick4", + "floralwhite", + "forestgreen", + "gainsboro", + "ghostwhite", + "gold", + "gold1", + "gold2", + "gold3", + "gold4", + "goldenrod", + "goldenrod1", + "goldenrod2", + "goldenrod3", + "goldenrod4", + "gray", + "gray0", + "gray1", + "gray2", + "gray3", + "gray4", + "gray5", + "gray6", + "gray7", + "gray8", + "gray9", + "gray10", + "gray11", + "gray12", + "gray13", + "gray14", + "gray15", + "gray16", + "gray17", + "gray18", + "gray19", + "gray20", + "gray21", + "gray22", + "gray23", + "gray24", + "gray25", + "gray26", + "gray27", + "gray28", + "gray29", + "gray30", + "gray31", + "gray32", + "gray33", + "gray34", + "gray35", + "gray36", + "gray37", + "gray38", + "gray39", + "gray40", + "gray41", + "gray42", + "gray43", + "gray44", + "gray45", + "gray46", + "gray47", + "gray48", + "gray49", + "gray50", + "gray51", + "gray52", + "gray53", + "gray54", + "gray55", + "gray56", + "gray57", + "gray58", + "gray59", + "gray60", + "gray61", + "gray62", + "gray63", + "gray64", + "gray65", + "gray66", + "gray67", + "gray68", + "gray69", + "gray70", + "gray71", + "gray72", + "gray73", + "gray74", + "gray75", + "gray76", + "gray77", + "gray78", + "gray79", + "gray80", + "gray81", + "gray82", + "gray83", + "gray84", + "gray85", + "gray86", + "gray87", + "gray88", + "gray89", + "gray90", + "gray91", + "gray92", + "gray93", + "gray94", + "gray95", + "gray96", + "gray97", + "gray98", + "gray99", + "gray100", + "green", + "green1", + "green2", + "green3", + "green4", + "greenyellow", + "grey", + "grey0", + "grey1", + "grey2", + "grey3", + "grey4", + "grey5", + "grey6", + "grey7", + "grey8", + "grey9", + "grey10", + "grey11", + "grey12", + "grey13", + "grey14", + "grey15", + "grey16", + "grey17", + "grey18", + "grey19", + "grey20", + "grey21", + "grey22", + "grey23", + "grey24", + "grey25", + "grey26", + "grey27", + "grey28", + "grey29", + "grey30", + "grey31", + "grey32", + "grey33", + "grey34", + "grey35", + "grey36", + "grey37", + "grey38", + "grey39", + "grey40", + "grey41", + "grey42", + "grey43", + "grey44", + "grey45", + "grey46", + "grey47", + "grey48", + "grey49", + "grey50", + "grey51", + "grey52", + "grey53", + "grey54", + "grey55", + "grey56", + "grey57", + "grey58", + "grey59", + "grey60", + "grey61", + "grey62", + "grey63", + "grey64", + "grey65", + "grey66", + "grey67", + "grey68", + "grey69", + "grey70", + "grey71", + "grey72", + "grey73", + "grey74", + "grey75", + "grey76", + "grey77", + "grey78", + "grey79", + "grey80", + "grey81", + "grey82", + "grey83", + "grey84", + "grey85", + "grey86", + "grey87", + "grey88", + "grey89", + "grey90", + "grey91", + "grey92", + "grey93", + "grey94", + "grey95", + "grey96", + "grey97", + "grey98", + "grey99", + "grey100", + "honeydew", + "honeydew1", + "honeydew2", + "honeydew3", + "honeydew4", + "hotpink", + "hotpink1", + "hotpink2", + "hotpink3", + "hotpink4", + "indianred", + "indianred1", + "indianred2", + "indianred3", + "indianred4", + "ivory", + "ivory1", + "ivory2", + "ivory3", + "ivory4", + "khaki", + "khaki1", + "khaki2", + "khaki3", + "khaki4", + "lavender", + "lavenderblush", + "lavenderblush1", + "lavenderblush2", + "lavenderblush3", + "lavenderblush4", + "lawngreen", + "lemonchiffon", + "lemonchiffon1", + "lemonchiffon2", + "lemonchiffon3", + "lemonchiffon4", + "lightblue", + "lightblue1", + "lightblue2", + "lightblue3", + "lightblue4", + "lightcoral", + "lightcyan", + "lightcyan1", + "lightcyan2", + "lightcyan3", + "lightcyan4", + "lightgoldenrod", + "lightgoldenrod1", + "lightgoldenrod2", + "lightgoldenrod3", + "lightgoldenrod4", + "lightgoldenrodyellow", + "lightgray", + "lightgreen", + "lightgrey", + "lightpink", + "lightpink1", + "lightpink2", + "lightpink3", + "lightpink4", + "lightsalmon", + "lightsalmon1", + "lightsalmon2", + "lightsalmon3", + "lightsalmon4", + "lightseagreen", + "lightskyblue", + "lightskyblue1", + "lightskyblue2", + "lightskyblue3", + "lightskyblue4", + "lightslateblue", + "lightslategray", + "lightslategrey", + "lightsteelblue", + "lightsteelblue1", + "lightsteelblue2", + "lightsteelblue3", + "lightsteelblue4", + "lightyellow", + "lightyellow1", + "lightyellow2", + "lightyellow3", + "lightyellow4", + "limegreen", + "linen", + "magenta", + "magenta1", + "magenta2", + "magenta3", + "magenta4", + "maroon", + "maroon1", + "maroon2", + "maroon3", + "maroon4", + "mediumaquamarine", + "mediumblue", + "mediumorchid", + "mediumorchid1", + "mediumorchid2", + "mediumorchid3", + "mediumorchid4", + "mediumpurple", + "mediumpurple1", + "mediumpurple2", + "mediumpurple3", + "mediumpurple4", + "mediumseagreen", + "mediumslateblue", + "mediumspringgreen", + "mediumturquoise", + "mediumvioletred", + "midnightblue", + "mintcream", + "mistyrose", + "mistyrose1", + "mistyrose2", + "mistyrose3", + "mistyrose4", + "moccasin", + "navajowhite", + "navajowhite1", + "navajowhite2", + "navajowhite3", + "navajowhite4", + "navy", + "navyblue", + "oldlace", + "olivedrab", + "olivedrab1", + "olivedrab2", + "olivedrab3", + "olivedrab4", + "orange", + "orange1", + "orange2", + "orange3", + "orange4", + "orangered", + "orangered1", + "orangered2", + "orangered3", + "orangered4", + "orchid", + "orchid1", + "orchid2", + "orchid3", + "orchid4", + "palegoldenrod", + "palegreen", + "palegreen1", + "palegreen2", + "palegreen3", + "palegreen4", + "paleturquoise", + "paleturquoise1", + "paleturquoise2", + "paleturquoise3", + "paleturquoise4", + "palevioletred", + "palevioletred1", + "palevioletred2", + "palevioletred3", + "palevioletred4", + "papayawhip", + "peachpuff", + "peachpuff1", + "peachpuff2", + "peachpuff3", + "peachpuff4", + "peru", + "pink", + "pink1", + "pink2", + "pink3", + "pink4", + "plum", + "plum1", + "plum2", + "plum3", + "plum4", + "powderblue", + "purple", + "purple1", + "purple2", + "purple3", + "purple4", + "red", + "red1", + "red2", + "red3", + "red4", + "rosybrown", + "rosybrown1", + "rosybrown2", + "rosybrown3", + "rosybrown4", + "royalblue", + "royalblue1", + "royalblue2", + "royalblue3", + "royalblue4", + "saddlebrown", + "salmon", + "salmon1", + "salmon2", + "salmon3", + "salmon4", + "sandybrown", + "seagreen", + "seagreen1", + "seagreen2", + "seagreen3", + "seagreen4", + "seashell", + "seashell1", + "seashell2", + "seashell3", + "seashell4", + "sienna", + "sienna1", + "sienna2", + "sienna3", + "sienna4", + "skyblue", + "skyblue1", + "skyblue2", + "skyblue3", + "skyblue4", + "slateblue", + "slateblue1", + "slateblue2", + "slateblue3", + "slateblue4", + "slategray", + "slategray1", + "slategray2", + "slategray3", + "slategray4", + "slategrey", + "snow", + "snow1", + "snow2", + "snow3", + "snow4", + "springgreen", + "springgreen1", + "springgreen2", + "springgreen3", + "springgreen4", + "steelblue", + "steelblue1", + "steelblue2", + "steelblue3", + "steelblue4", + "tan", + "tan1", + "tan2", + "tan3", + "tan4", + "thistle", + "thistle1", + "thistle2", + "thistle3", + "thistle4", + "tomato", + "tomato1", + "tomato2", + "tomato3", + "tomato4", + "turquoise", + "turquoise1", + "turquoise2", + "turquoise3", + "turquoise4", + "violet", + "violetred", + "violetred1", + "violetred2", + "violetred3", + "violetred4", + "wheat", + "wheat1", + "wheat2", + "wheat3", + "wheat4", + "whitesmoke", + "yellow", + "yellow1", + "yellow2", + "yellow3", + "yellow4", + "yellowgreen" + ], + "defaultValue": "blue", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Color_of_Non_Significant_Genes", + "displayName": "Color of Non-Significant Genes", + "description": "", + "paramType": "SELECT", + "paramGroup": "Plot", + "paramValues": [ + "white", + "aliceblue", + "antiquewhite", + "antiquewhite1", + "antiquewhite2", + "antiquewhite3", + "antiquewhite4", + "aquamarine", + "aquamarine1", + "aquamarine2", + "aquamarine3", + "aquamarine4", + "azure", + "azure1", + "azure2", + "azure3", + "azure4", + "beige", + "bisque", + "bisque1", + "bisque2", + "bisque3", + "bisque4", + "black", + "blanchedalmond", + "blue", + "blue1", + "blue2", + "blue3", + "blue4", + "blueviolet", + "brown", + "brown1", + "brown2", + "brown3", + "brown4", + "burlywood", + "burlywood1", + "burlywood2", + "burlywood3", + "burlywood4", + "cadetblue", + "cadetblue1", + "cadetblue2", + "cadetblue3", + "cadetblue4", + "chartreuse", + "chartreuse1", + "chartreuse2", + "chartreuse3", + "chartreuse4", + "chocolate", + "chocolate1", + "chocolate2", + "chocolate3", + "chocolate4", + "coral", + "coral1", + "coral2", + "coral3", + "coral4", + "cornflowerblue", + "cornsilk", + "cornsilk1", + "cornsilk2", + "cornsilk3", + "cornsilk4", + "cyan", + "cyan1", + "cyan2", + "cyan3", + "cyan4", + "darkblue", + "darkcyan", + "darkgoldenrod", + "darkgoldenrod1", + "darkgoldenrod2", + "darkgoldenrod3", + "darkgoldenrod4", + "darkgray", + "darkgreen", + "darkgrey", + "darkkhaki", + "darkmagenta", + "darkolivegreen", + "darkolivegreen1", + "darkolivegreen2", + "darkolivegreen3", + "darkolivegreen4", + "darkorange", + "darkorange1", + "darkorange2", + "darkorange3", + "darkorange4", + "darkorchid", + "darkorchid1", + "darkorchid2", + "darkorchid3", + "darkorchid4", + "darkred", + "darksalmon", + "darkseagreen", + "darkseagreen1", + "darkseagreen2", + "darkseagreen3", + "darkseagreen4", + "darkslateblue", + "darkslategray", + "darkslategray1", + "darkslategray2", + "darkslategray3", + "darkslategray4", + "darkslategrey", + "darkturquoise", + "darkviolet", + "deeppink", + "deeppink1", + "deeppink2", + "deeppink3", + "deeppink4", + "deepskyblue", + "deepskyblue1", + "deepskyblue2", + "deepskyblue3", + "deepskyblue4", + "dimgray", + "dimgrey", + "dodgerblue", + "dodgerblue1", + "dodgerblue2", + "dodgerblue3", + "dodgerblue4", + "firebrick", + "firebrick1", + "firebrick2", + "firebrick3", + "firebrick4", + "floralwhite", + "forestgreen", + "gainsboro", + "ghostwhite", + "gold", + "gold1", + "gold2", + "gold3", + "gold4", + "goldenrod", + "goldenrod1", + "goldenrod2", + "goldenrod3", + "goldenrod4", + "gray", + "gray0", + "gray1", + "gray2", + "gray3", + "gray4", + "gray5", + "gray6", + "gray7", + "gray8", + "gray9", + "gray10", + "gray11", + "gray12", + "gray13", + "gray14", + "gray15", + "gray16", + "gray17", + "gray18", + "gray19", + "gray20", + "gray21", + "gray22", + "gray23", + "gray24", + "gray25", + "gray26", + "gray27", + "gray28", + "gray29", + "gray30", + "gray31", + "gray32", + "gray33", + "gray34", + "gray35", + "gray36", + "gray37", + "gray38", + "gray39", + "gray40", + "gray41", + "gray42", + "gray43", + "gray44", + "gray45", + "gray46", + "gray47", + "gray48", + "gray49", + "gray50", + "gray51", + "gray52", + "gray53", + "gray54", + "gray55", + "gray56", + "gray57", + "gray58", + "gray59", + "gray60", + "gray61", + "gray62", + "gray63", + "gray64", + "gray65", + "gray66", + "gray67", + "gray68", + "gray69", + "gray70", + "gray71", + "gray72", + "gray73", + "gray74", + "gray75", + "gray76", + "gray77", + "gray78", + "gray79", + "gray80", + "gray81", + "gray82", + "gray83", + "gray84", + "gray85", + "gray86", + "gray87", + "gray88", + "gray89", + "gray90", + "gray91", + "gray92", + "gray93", + "gray94", + "gray95", + "gray96", + "gray97", + "gray98", + "gray99", + "gray100", + "green", + "green1", + "green2", + "green3", + "green4", + "greenyellow", + "grey", + "grey0", + "grey1", + "grey2", + "grey3", + "grey4", + "grey5", + "grey6", + "grey7", + "grey8", + "grey9", + "grey10", + "grey11", + "grey12", + "grey13", + "grey14", + "grey15", + "grey16", + "grey17", + "grey18", + "grey19", + "grey20", + "grey21", + "grey22", + "grey23", + "grey24", + "grey25", + "grey26", + "grey27", + "grey28", + "grey29", + "grey30", + "grey31", + "grey32", + "grey33", + "grey34", + "grey35", + "grey36", + "grey37", + "grey38", + "grey39", + "grey40", + "grey41", + "grey42", + "grey43", + "grey44", + "grey45", + "grey46", + "grey47", + "grey48", + "grey49", + "grey50", + "grey51", + "grey52", + "grey53", + "grey54", + "grey55", + "grey56", + "grey57", + "grey58", + "grey59", + "grey60", + "grey61", + "grey62", + "grey63", + "grey64", + "grey65", + "grey66", + "grey67", + "grey68", + "grey69", + "grey70", + "grey71", + "grey72", + "grey73", + "grey74", + "grey75", + "grey76", + "grey77", + "grey78", + "grey79", + "grey80", + "grey81", + "grey82", + "grey83", + "grey84", + "grey85", + "grey86", + "grey87", + "grey88", + "grey89", + "grey90", + "grey91", + "grey92", + "grey93", + "grey94", + "grey95", + "grey96", + "grey97", + "grey98", + "grey99", + "grey100", + "honeydew", + "honeydew1", + "honeydew2", + "honeydew3", + "honeydew4", + "hotpink", + "hotpink1", + "hotpink2", + "hotpink3", + "hotpink4", + "indianred", + "indianred1", + "indianred2", + "indianred3", + "indianred4", + "ivory", + "ivory1", + "ivory2", + "ivory3", + "ivory4", + "khaki", + "khaki1", + "khaki2", + "khaki3", + "khaki4", + "lavender", + "lavenderblush", + "lavenderblush1", + "lavenderblush2", + "lavenderblush3", + "lavenderblush4", + "lawngreen", + "lemonchiffon", + "lemonchiffon1", + "lemonchiffon2", + "lemonchiffon3", + "lemonchiffon4", + "lightblue", + "lightblue1", + "lightblue2", + "lightblue3", + "lightblue4", + "lightcoral", + "lightcyan", + "lightcyan1", + "lightcyan2", + "lightcyan3", + "lightcyan4", + "lightgoldenrod", + "lightgoldenrod1", + "lightgoldenrod2", + "lightgoldenrod3", + "lightgoldenrod4", + "lightgoldenrodyellow", + "lightgray", + "lightgreen", + "lightgrey", + "lightpink", + "lightpink1", + "lightpink2", + "lightpink3", + "lightpink4", + "lightsalmon", + "lightsalmon1", + "lightsalmon2", + "lightsalmon3", + "lightsalmon4", + "lightseagreen", + "lightskyblue", + "lightskyblue1", + "lightskyblue2", + "lightskyblue3", + "lightskyblue4", + "lightslateblue", + "lightslategray", + "lightslategrey", + "lightsteelblue", + "lightsteelblue1", + "lightsteelblue2", + "lightsteelblue3", + "lightsteelblue4", + "lightyellow", + "lightyellow1", + "lightyellow2", + "lightyellow3", + "lightyellow4", + "limegreen", + "linen", + "magenta", + "magenta1", + "magenta2", + "magenta3", + "magenta4", + "maroon", + "maroon1", + "maroon2", + "maroon3", + "maroon4", + "mediumaquamarine", + "mediumblue", + "mediumorchid", + "mediumorchid1", + "mediumorchid2", + "mediumorchid3", + "mediumorchid4", + "mediumpurple", + "mediumpurple1", + "mediumpurple2", + "mediumpurple3", + "mediumpurple4", + "mediumseagreen", + "mediumslateblue", + "mediumspringgreen", + "mediumturquoise", + "mediumvioletred", + "midnightblue", + "mintcream", + "mistyrose", + "mistyrose1", + "mistyrose2", + "mistyrose3", + "mistyrose4", + "moccasin", + "navajowhite", + "navajowhite1", + "navajowhite2", + "navajowhite3", + "navajowhite4", + "navy", + "navyblue", + "oldlace", + "olivedrab", + "olivedrab1", + "olivedrab2", + "olivedrab3", + "olivedrab4", + "orange", + "orange1", + "orange2", + "orange3", + "orange4", + "orangered", + "orangered1", + "orangered2", + "orangered3", + "orangered4", + "orchid", + "orchid1", + "orchid2", + "orchid3", + "orchid4", + "palegoldenrod", + "palegreen", + "palegreen1", + "palegreen2", + "palegreen3", + "palegreen4", + "paleturquoise", + "paleturquoise1", + "paleturquoise2", + "paleturquoise3", + "paleturquoise4", + "palevioletred", + "palevioletred1", + "palevioletred2", + "palevioletred3", + "palevioletred4", + "papayawhip", + "peachpuff", + "peachpuff1", + "peachpuff2", + "peachpuff3", + "peachpuff4", + "peru", + "pink", + "pink1", + "pink2", + "pink3", + "pink4", + "plum", + "plum1", + "plum2", + "plum3", + "plum4", + "powderblue", + "purple", + "purple1", + "purple2", + "purple3", + "purple4", + "red", + "red1", + "red2", + "red3", + "red4", + "rosybrown", + "rosybrown1", + "rosybrown2", + "rosybrown3", + "rosybrown4", + "royalblue", + "royalblue1", + "royalblue2", + "royalblue3", + "royalblue4", + "saddlebrown", + "salmon", + "salmon1", + "salmon2", + "salmon3", + "salmon4", + "sandybrown", + "seagreen", + "seagreen1", + "seagreen2", + "seagreen3", + "seagreen4", + "seashell", + "seashell1", + "seashell2", + "seashell3", + "seashell4", + "sienna", + "sienna1", + "sienna2", + "sienna3", + "sienna4", + "skyblue", + "skyblue1", + "skyblue2", + "skyblue3", + "skyblue4", + "slateblue", + "slateblue1", + "slateblue2", + "slateblue3", + "slateblue4", + "slategray", + "slategray1", + "slategray2", + "slategray3", + "slategray4", + "slategrey", + "snow", + "snow1", + "snow2", + "snow3", + "snow4", + "springgreen", + "springgreen1", + "springgreen2", + "springgreen3", + "springgreen4", + "steelblue", + "steelblue1", + "steelblue2", + "steelblue3", + "steelblue4", + "tan", + "tan1", + "tan2", + "tan3", + "tan4", + "thistle", + "thistle1", + "thistle2", + "thistle3", + "thistle4", + "tomato", + "tomato1", + "tomato2", + "tomato3", + "tomato4", + "turquoise", + "turquoise1", + "turquoise2", + "turquoise3", + "turquoise4", + "violet", + "violetred", + "violetred1", + "violetred2", + "violetred3", + "violetred4", + "wheat", + "wheat1", + "wheat2", + "wheat3", + "wheat4", + "whitesmoke", + "yellow", + "yellow1", + "yellow2", + "yellow3", + "yellow4", + "yellowgreen" + ], + "defaultValue": "black", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Color_of_Log_Fold_Change_Threshold_Line", + "displayName": "Color of Log Fold Change Threshold Line", + "description": "The color of the vertical fold-change threshold lines", + "paramType": "SELECT", + "paramGroup": "Plot", + "paramValues": [ + "white", + "aliceblue", + "antiquewhite", + "antiquewhite1", + "antiquewhite2", + "antiquewhite3", + "antiquewhite4", + "aquamarine", + "aquamarine1", + "aquamarine2", + "aquamarine3", + "aquamarine4", + "azure", + "azure1", + "azure2", + "azure3", + "azure4", + "beige", + "bisque", + "bisque1", + "bisque2", + "bisque3", + "bisque4", + "black", + "blanchedalmond", + "blue", + "blue1", + "blue2", + "blue3", + "blue4", + "blueviolet", + "brown", + "brown1", + "brown2", + "brown3", + "brown4", + "burlywood", + "burlywood1", + "burlywood2", + "burlywood3", + "burlywood4", + "cadetblue", + "cadetblue1", + "cadetblue2", + "cadetblue3", + "cadetblue4", + "chartreuse", + "chartreuse1", + "chartreuse2", + "chartreuse3", + "chartreuse4", + "chocolate", + "chocolate1", + "chocolate2", + "chocolate3", + "chocolate4", + "coral", + "coral1", + "coral2", + "coral3", + "coral4", + "cornflowerblue", + "cornsilk", + "cornsilk1", + "cornsilk2", + "cornsilk3", + "cornsilk4", + "cyan", + "cyan1", + "cyan2", + "cyan3", + "cyan4", + "darkblue", + "darkcyan", + "darkgoldenrod", + "darkgoldenrod1", + "darkgoldenrod2", + "darkgoldenrod3", + "darkgoldenrod4", + "darkgray", + "darkgreen", + "darkgrey", + "darkkhaki", + "darkmagenta", + "darkolivegreen", + "darkolivegreen1", + "darkolivegreen2", + "darkolivegreen3", + "darkolivegreen4", + "darkorange", + "darkorange1", + "darkorange2", + "darkorange3", + "darkorange4", + "darkorchid", + "darkorchid1", + "darkorchid2", + "darkorchid3", + "darkorchid4", + "darkred", + "darksalmon", + "darkseagreen", + "darkseagreen1", + "darkseagreen2", + "darkseagreen3", + "darkseagreen4", + "darkslateblue", + "darkslategray", + "darkslategray1", + "darkslategray2", + "darkslategray3", + "darkslategray4", + "darkslategrey", + "darkturquoise", + "darkviolet", + "deeppink", + "deeppink1", + "deeppink2", + "deeppink3", + "deeppink4", + "deepskyblue", + "deepskyblue1", + "deepskyblue2", + "deepskyblue3", + "deepskyblue4", + "dimgray", + "dimgrey", + "dodgerblue", + "dodgerblue1", + "dodgerblue2", + "dodgerblue3", + "dodgerblue4", + "firebrick", + "firebrick1", + "firebrick2", + "firebrick3", + "firebrick4", + "floralwhite", + "forestgreen", + "gainsboro", + "ghostwhite", + "gold", + "gold1", + "gold2", + "gold3", + "gold4", + "goldenrod", + "goldenrod1", + "goldenrod2", + "goldenrod3", + "goldenrod4", + "gray", + "gray0", + "gray1", + "gray2", + "gray3", + "gray4", + "gray5", + "gray6", + "gray7", + "gray8", + "gray9", + "gray10", + "gray11", + "gray12", + "gray13", + "gray14", + "gray15", + "gray16", + "gray17", + "gray18", + "gray19", + "gray20", + "gray21", + "gray22", + "gray23", + "gray24", + "gray25", + "gray26", + "gray27", + "gray28", + "gray29", + "gray30", + "gray31", + "gray32", + "gray33", + "gray34", + "gray35", + "gray36", + "gray37", + "gray38", + "gray39", + "gray40", + "gray41", + "gray42", + "gray43", + "gray44", + "gray45", + "gray46", + "gray47", + "gray48", + "gray49", + "gray50", + "gray51", + "gray52", + "gray53", + "gray54", + "gray55", + "gray56", + "gray57", + "gray58", + "gray59", + "gray60", + "gray61", + "gray62", + "gray63", + "gray64", + "gray65", + "gray66", + "gray67", + "gray68", + "gray69", + "gray70", + "gray71", + "gray72", + "gray73", + "gray74", + "gray75", + "gray76", + "gray77", + "gray78", + "gray79", + "gray80", + "gray81", + "gray82", + "gray83", + "gray84", + "gray85", + "gray86", + "gray87", + "gray88", + "gray89", + "gray90", + "gray91", + "gray92", + "gray93", + "gray94", + "gray95", + "gray96", + "gray97", + "gray98", + "gray99", + "gray100", + "green", + "green1", + "green2", + "green3", + "green4", + "greenyellow", + "grey", + "grey0", + "grey1", + "grey2", + "grey3", + "grey4", + "grey5", + "grey6", + "grey7", + "grey8", + "grey9", + "grey10", + "grey11", + "grey12", + "grey13", + "grey14", + "grey15", + "grey16", + "grey17", + "grey18", + "grey19", + "grey20", + "grey21", + "grey22", + "grey23", + "grey24", + "grey25", + "grey26", + "grey27", + "grey28", + "grey29", + "grey30", + "grey31", + "grey32", + "grey33", + "grey34", + "grey35", + "grey36", + "grey37", + "grey38", + "grey39", + "grey40", + "grey41", + "grey42", + "grey43", + "grey44", + "grey45", + "grey46", + "grey47", + "grey48", + "grey49", + "grey50", + "grey51", + "grey52", + "grey53", + "grey54", + "grey55", + "grey56", + "grey57", + "grey58", + "grey59", + "grey60", + "grey61", + "grey62", + "grey63", + "grey64", + "grey65", + "grey66", + "grey67", + "grey68", + "grey69", + "grey70", + "grey71", + "grey72", + "grey73", + "grey74", + "grey75", + "grey76", + "grey77", + "grey78", + "grey79", + "grey80", + "grey81", + "grey82", + "grey83", + "grey84", + "grey85", + "grey86", + "grey87", + "grey88", + "grey89", + "grey90", + "grey91", + "grey92", + "grey93", + "grey94", + "grey95", + "grey96", + "grey97", + "grey98", + "grey99", + "grey100", + "honeydew", + "honeydew1", + "honeydew2", + "honeydew3", + "honeydew4", + "hotpink", + "hotpink1", + "hotpink2", + "hotpink3", + "hotpink4", + "indianred", + "indianred1", + "indianred2", + "indianred3", + "indianred4", + "ivory", + "ivory1", + "ivory2", + "ivory3", + "ivory4", + "khaki", + "khaki1", + "khaki2", + "khaki3", + "khaki4", + "lavender", + "lavenderblush", + "lavenderblush1", + "lavenderblush2", + "lavenderblush3", + "lavenderblush4", + "lawngreen", + "lemonchiffon", + "lemonchiffon1", + "lemonchiffon2", + "lemonchiffon3", + "lemonchiffon4", + "lightblue", + "lightblue1", + "lightblue2", + "lightblue3", + "lightblue4", + "lightcoral", + "lightcyan", + "lightcyan1", + "lightcyan2", + "lightcyan3", + "lightcyan4", + "lightgoldenrod", + "lightgoldenrod1", + "lightgoldenrod2", + "lightgoldenrod3", + "lightgoldenrod4", + "lightgoldenrodyellow", + "lightgray", + "lightgreen", + "lightgrey", + "lightpink", + "lightpink1", + "lightpink2", + "lightpink3", + "lightpink4", + "lightsalmon", + "lightsalmon1", + "lightsalmon2", + "lightsalmon3", + "lightsalmon4", + "lightseagreen", + "lightskyblue", + "lightskyblue1", + "lightskyblue2", + "lightskyblue3", + "lightskyblue4", + "lightslateblue", + "lightslategray", + "lightslategrey", + "lightsteelblue", + "lightsteelblue1", + "lightsteelblue2", + "lightsteelblue3", + "lightsteelblue4", + "lightyellow", + "lightyellow1", + "lightyellow2", + "lightyellow3", + "lightyellow4", + "limegreen", + "linen", + "magenta", + "magenta1", + "magenta2", + "magenta3", + "magenta4", + "maroon", + "maroon1", + "maroon2", + "maroon3", + "maroon4", + "mediumaquamarine", + "mediumblue", + "mediumorchid", + "mediumorchid1", + "mediumorchid2", + "mediumorchid3", + "mediumorchid4", + "mediumpurple", + "mediumpurple1", + "mediumpurple2", + "mediumpurple3", + "mediumpurple4", + "mediumseagreen", + "mediumslateblue", + "mediumspringgreen", + "mediumturquoise", + "mediumvioletred", + "midnightblue", + "mintcream", + "mistyrose", + "mistyrose1", + "mistyrose2", + "mistyrose3", + "mistyrose4", + "moccasin", + "navajowhite", + "navajowhite1", + "navajowhite2", + "navajowhite3", + "navajowhite4", + "navy", + "navyblue", + "oldlace", + "olivedrab", + "olivedrab1", + "olivedrab2", + "olivedrab3", + "olivedrab4", + "orange", + "orange1", + "orange2", + "orange3", + "orange4", + "orangered", + "orangered1", + "orangered2", + "orangered3", + "orangered4", + "orchid", + "orchid1", + "orchid2", + "orchid3", + "orchid4", + "palegoldenrod", + "palegreen", + "palegreen1", + "palegreen2", + "palegreen3", + "palegreen4", + "paleturquoise", + "paleturquoise1", + "paleturquoise2", + "paleturquoise3", + "paleturquoise4", + "palevioletred", + "palevioletred1", + "palevioletred2", + "palevioletred3", + "palevioletred4", + "papayawhip", + "peachpuff", + "peachpuff1", + "peachpuff2", + "peachpuff3", + "peachpuff4", + "peru", + "pink", + "pink1", + "pink2", + "pink3", + "pink4", + "plum", + "plum1", + "plum2", + "plum3", + "plum4", + "powderblue", + "purple", + "purple1", + "purple2", + "purple3", + "purple4", + "red", + "red1", + "red2", + "red3", + "red4", + "rosybrown", + "rosybrown1", + "rosybrown2", + "rosybrown3", + "rosybrown4", + "royalblue", + "royalblue1", + "royalblue2", + "royalblue3", + "royalblue4", + "saddlebrown", + "salmon", + "salmon1", + "salmon2", + "salmon3", + "salmon4", + "sandybrown", + "seagreen", + "seagreen1", + "seagreen2", + "seagreen3", + "seagreen4", + "seashell", + "seashell1", + "seashell2", + "seashell3", + "seashell4", + "sienna", + "sienna1", + "sienna2", + "sienna3", + "sienna4", + "skyblue", + "skyblue1", + "skyblue2", + "skyblue3", + "skyblue4", + "slateblue", + "slateblue1", + "slateblue2", + "slateblue3", + "slateblue4", + 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"displayName": "Color of Genes Meeting Only P-Value Threshold", + "description": "", + "paramType": "SELECT", + "paramGroup": "Plot", + "paramValues": [ + "white", + "aliceblue", + "antiquewhite", + "antiquewhite1", + "antiquewhite2", + "antiquewhite3", + "antiquewhite4", + "aquamarine", + "aquamarine1", + "aquamarine2", + "aquamarine3", + "aquamarine4", + "azure", + "azure1", + "azure2", + "azure3", + "azure4", + "beige", + "bisque", + "bisque1", + "bisque2", + "bisque3", + "bisque4", + "black", + "blanchedalmond", + "blue", + "blue1", + "blue2", + "blue3", + "blue4", + "blueviolet", + "brown", + "brown1", + "brown2", + "brown3", + "brown4", + "burlywood", + "burlywood1", + "burlywood2", + "burlywood3", + "burlywood4", + "cadetblue", + "cadetblue1", + "cadetblue2", + "cadetblue3", + "cadetblue4", + "chartreuse", + "chartreuse1", + "chartreuse2", + "chartreuse3", + "chartreuse4", + "chocolate", + "chocolate1", + "chocolate2", + "chocolate3", + "chocolate4", + "coral", + "coral1", + 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"gray41", + "gray42", + "gray43", + "gray44", + "gray45", + "gray46", + "gray47", + "gray48", + "gray49", + "gray50", + "gray51", + "gray52", + "gray53", + "gray54", + "gray55", + "gray56", + "gray57", + "gray58", + "gray59", + "gray60", + "gray61", + "gray62", + "gray63", + "gray64", + "gray65", + "gray66", + "gray67", + "gray68", + "gray69", + "gray70", + "gray71", + "gray72", + "gray73", + "gray74", + "gray75", + "gray76", + "gray77", + "gray78", + "gray79", + "gray80", + "gray81", + "gray82", + "gray83", + "gray84", + "gray85", + "gray86", + "gray87", + "gray88", + "gray89", + "gray90", + "gray91", + "gray92", + "gray93", + "gray94", + "gray95", + "gray96", + "gray97", + "gray98", + "gray99", + "gray100", + "green", + "green1", + "green2", + "green3", + "green4", + "greenyellow", + "grey", + "grey0", + "grey1", + "grey2", + "grey3", + "grey4", + "grey5", + "grey6", + "grey7", + "grey8", + "grey9", + "grey10", + "grey11", + "grey12", + "grey13", + "grey14", + "grey15", + "grey16", + 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"lightpink4", + "lightsalmon", + "lightsalmon1", + "lightsalmon2", + "lightsalmon3", + "lightsalmon4", + "lightseagreen", + "lightskyblue", + "lightskyblue1", + "lightskyblue2", + "lightskyblue3", + "lightskyblue4", + "lightslateblue", + "lightslategray", + "lightslategrey", + "lightsteelblue", + "lightsteelblue1", + "lightsteelblue2", + "lightsteelblue3", + "lightsteelblue4", + "lightyellow", + "lightyellow1", + "lightyellow2", + "lightyellow3", + "lightyellow4", + "limegreen", + "linen", + "magenta", + "magenta1", + "magenta2", + "magenta3", + "magenta4", + "maroon", + "maroon1", + "maroon2", + "maroon3", + "maroon4", + "mediumaquamarine", + "mediumblue", + "mediumorchid", + "mediumorchid1", + "mediumorchid2", + "mediumorchid3", + "mediumorchid4", + "mediumpurple", + "mediumpurple1", + "mediumpurple2", + "mediumpurple3", + "mediumpurple4", + "mediumseagreen", + "mediumslateblue", + "mediumspringgreen", + "mediumturquoise", + "mediumvioletred", + "midnightblue", + "mintcream", + "mistyrose", + "mistyrose1", + "mistyrose2", + "mistyrose3", + "mistyrose4", + "moccasin", + "navajowhite", + "navajowhite1", + "navajowhite2", + "navajowhite3", + "navajowhite4", + "navy", + "navyblue", + "oldlace", + "olivedrab", + "olivedrab1", + "olivedrab2", + "olivedrab3", + "olivedrab4", + "orange", + "orange1", + "orange2", + "orange3", + "orange4", + "orangered", + "orangered1", + "orangered2", + "orangered3", + "orangered4", + "orchid", + "orchid1", + "orchid2", + "orchid3", + "orchid4", + "palegoldenrod", + "palegreen", + "palegreen1", + "palegreen2", + "palegreen3", + "palegreen4", + "paleturquoise", + "paleturquoise1", + "paleturquoise2", + "paleturquoise3", + "paleturquoise4", + "palevioletred", + "palevioletred1", + "palevioletred2", + "palevioletred3", + "palevioletred4", + "papayawhip", + "peachpuff", + "peachpuff1", + "peachpuff2", + "peachpuff3", + "peachpuff4", + "peru", + "pink", + "pink1", + "pink2", + "pink3", + "pink4", + "plum", + "plum1", + "plum2", + "plum3", + "plum4", + "powderblue", + "purple", + "purple1", + "purple2", + "purple3", + "purple4", + "red", + "red1", + "red2", + "red3", + "red4", + "rosybrown", + "rosybrown1", + "rosybrown2", + "rosybrown3", + "rosybrown4", + "royalblue", + "royalblue1", + "royalblue2", + "royalblue3", + "royalblue4", + "saddlebrown", + "salmon", + "salmon1", + "salmon2", + "salmon3", + "salmon4", + "sandybrown", + "seagreen", + "seagreen1", + "seagreen2", + "seagreen3", + "seagreen4", + "seashell", + "seashell1", + "seashell2", + "seashell3", + "seashell4", + "sienna", + "sienna1", + "sienna2", + "sienna3", + "sienna4", + "skyblue", + "skyblue1", + "skyblue2", + "skyblue3", + "skyblue4", + "slateblue", + "slateblue1", + "slateblue2", + "slateblue3", + "slateblue4", + "slategray", + "slategray1", + "slategray2", + "slategray3", + "slategray4", + "slategrey", + "snow", + "snow1", + "snow2", + "snow3", + "snow4", + "springgreen", + "springgreen1", + "springgreen2", + "springgreen3", + "springgreen4", + "steelblue", + "steelblue1", + "steelblue2", + "steelblue3", + "steelblue4", + "tan", + "tan1", + "tan2", + "tan3", + "tan4", + "thistle", + "thistle1", + "thistle2", + "thistle3", + "thistle4", + "tomato", + "tomato1", + "tomato2", + "tomato3", + "tomato4", + "turquoise", + "turquoise1", + "turquoise2", + "turquoise3", + "turquoise4", + "violet", + "violetred", + "violetred1", + "violetred2", + "violetred3", + "violetred4", + "wheat", + "wheat1", + "wheat2", + "wheat3", + "wheat4", + "whitesmoke", + "yellow", + "yellow1", + "yellow2", + "yellow3", + "yellow4", + "yellowgreen" + ], + "defaultValue": "lightgoldenrod2", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "color_for_genes_meeting_p_value_and_fold_change_thresholds", + "displayName": "Color for genes meeting p-value and fold-change thresholds", + "description": "", + "paramType": "SELECT", + "paramGroup": "Plot", + "paramValues": [ + "white", + "aliceblue", + "antiquewhite", + 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"darkcyan", + "darkgoldenrod", + "darkgoldenrod1", + "darkgoldenrod2", + "darkgoldenrod3", + "darkgoldenrod4", + "darkgray", + "darkgreen", + "darkgrey", + "darkkhaki", + "darkmagenta", + "darkolivegreen", + "darkolivegreen1", + "darkolivegreen2", + "darkolivegreen3", + "darkolivegreen4", + "darkorange", + "darkorange1", + "darkorange2", + "darkorange3", + "darkorange4", + "darkorchid", + "darkorchid1", + "darkorchid2", + "darkorchid3", + "darkorchid4", + "darkred", + "darksalmon", + "darkseagreen", + "darkseagreen1", + "darkseagreen2", + "darkseagreen3", + "darkseagreen4", + "darkslateblue", + "darkslategray", + "darkslategray1", + "darkslategray2", + "darkslategray3", + "darkslategray4", + "darkslategrey", + "darkturquoise", + "darkviolet", + "deeppink", + "deeppink1", + "deeppink2", + "deeppink3", + "deeppink4", + "deepskyblue", + "deepskyblue1", + "deepskyblue2", + "deepskyblue3", + "deepskyblue4", + "dimgray", + "dimgrey", + "dodgerblue", + "dodgerblue1", + "dodgerblue2", + "dodgerblue3", + "dodgerblue4", + "firebrick", + "firebrick1", + "firebrick2", + "firebrick3", + "firebrick4", + "floralwhite", + "forestgreen", + "gainsboro", + "ghostwhite", + "gold", + "gold1", + "gold2", + "gold3", + "gold4", + "goldenrod", + "goldenrod1", + "goldenrod2", + "goldenrod3", + "goldenrod4", + "gray", + "gray0", + "gray1", + "gray2", + "gray3", + "gray4", + "gray5", + "gray6", + "gray7", + "gray8", + "gray9", + "gray10", + "gray11", + "gray12", + "gray13", + "gray14", + "gray15", + "gray16", + "gray17", + "gray18", + "gray19", + "gray20", + "gray21", + "gray22", + "gray23", + "gray24", + "gray25", + "gray26", + "gray27", + "gray28", + "gray29", + "gray30", + "gray31", + "gray32", + "gray33", + "gray34", + "gray35", + "gray36", + "gray37", + "gray38", + "gray39", + "gray40", + "gray41", + "gray42", + "gray43", + "gray44", + "gray45", + "gray46", + "gray47", + "gray48", + "gray49", + "gray50", + "gray51", + "gray52", + "gray53", + "gray54", + "gray55", + "gray56", + "gray57", + "gray58", + "gray59", + "gray60", + "gray61", + "gray62", + "gray63", + "gray64", + "gray65", + "gray66", + "gray67", + "gray68", + "gray69", + "gray70", + "gray71", + "gray72", + "gray73", + "gray74", + "gray75", + "gray76", + "gray77", + "gray78", + "gray79", + "gray80", + "gray81", + "gray82", + "gray83", + "gray84", + "gray85", + "gray86", + "gray87", + "gray88", + "gray89", + "gray90", + "gray91", + "gray92", + "gray93", + "gray94", + "gray95", + "gray96", + "gray97", + "gray98", + "gray99", + "gray100", + "green", + "green1", + "green2", + "green3", + "green4", + "greenyellow", + "grey", + "grey0", + "grey1", + "grey2", + "grey3", + "grey4", + "grey5", + "grey6", + "grey7", + "grey8", + "grey9", + "grey10", + "grey11", + "grey12", + "grey13", + "grey14", + "grey15", + "grey16", + "grey17", + "grey18", + "grey19", + "grey20", + "grey21", + "grey22", + "grey23", + "grey24", + "grey25", + "grey26", + "grey27", + "grey28", + "grey29", + "grey30", + "grey31", + "grey32", + 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"indianred2", + "indianred3", + "indianred4", + "ivory", + "ivory1", + "ivory2", + "ivory3", + "ivory4", + "khaki", + "khaki1", + "khaki2", + "khaki3", + "khaki4", + "lavender", + "lavenderblush", + "lavenderblush1", + "lavenderblush2", + "lavenderblush3", + "lavenderblush4", + "lawngreen", + "lemonchiffon", + "lemonchiffon1", + "lemonchiffon2", + "lemonchiffon3", + "lemonchiffon4", + "lightblue", + "lightblue1", + "lightblue2", + "lightblue3", + "lightblue4", + "lightcoral", + "lightcyan", + "lightcyan1", + "lightcyan2", + "lightcyan3", + "lightcyan4", + "lightgoldenrod", + "lightgoldenrod1", + "lightgoldenrod2", + "lightgoldenrod3", + "lightgoldenrod4", + "lightgoldenrodyellow", + "lightgray", + "lightgreen", + "lightgrey", + "lightpink", + "lightpink1", + "lightpink2", + "lightpink3", + "lightpink4", + "lightsalmon", + "lightsalmon1", + "lightsalmon2", + "lightsalmon3", + "lightsalmon4", + "lightseagreen", + "lightskyblue", + "lightskyblue1", + "lightskyblue2", + "lightskyblue3", + "lightskyblue4", + "lightslateblue", + "lightslategray", + "lightslategrey", + "lightsteelblue", + "lightsteelblue1", + "lightsteelblue2", + "lightsteelblue3", + "lightsteelblue4", + "lightyellow", + "lightyellow1", + "lightyellow2", + "lightyellow3", + "lightyellow4", + "limegreen", + "linen", + "magenta", + "magenta1", + "magenta2", + "magenta3", + "magenta4", + "maroon", + "maroon1", + "maroon2", + "maroon3", + "maroon4", + "mediumaquamarine", + "mediumblue", + "mediumorchid", + "mediumorchid1", + "mediumorchid2", + "mediumorchid3", + "mediumorchid4", + "mediumpurple", + "mediumpurple1", + "mediumpurple2", + "mediumpurple3", + "mediumpurple4", + "mediumseagreen", + "mediumslateblue", + "mediumspringgreen", + "mediumturquoise", + "mediumvioletred", + "midnightblue", + "mintcream", + "mistyrose", + "mistyrose1", + "mistyrose2", + "mistyrose3", + "mistyrose4", + "moccasin", + "navajowhite", + "navajowhite1", + "navajowhite2", + "navajowhite3", + "navajowhite4", + "navy", + "navyblue", + "oldlace", + "olivedrab", + "olivedrab1", + "olivedrab2", + "olivedrab3", + "olivedrab4", + "orange", + "orange1", + "orange2", + "orange3", + "orange4", + "orangered", + "orangered1", + "orangered2", + "orangered3", + "orangered4", + "orchid", + "orchid1", + "orchid2", + "orchid3", + "orchid4", + "palegoldenrod", + "palegreen", + "palegreen1", + "palegreen2", + "palegreen3", + "palegreen4", + "paleturquoise", + "paleturquoise1", + "paleturquoise2", + "paleturquoise3", + "paleturquoise4", + "palevioletred", + "palevioletred1", + "palevioletred2", + "palevioletred3", + "palevioletred4", + "papayawhip", + "peachpuff", + "peachpuff1", + "peachpuff2", + "peachpuff3", + "peachpuff4", + "peru", + "pink", + "pink1", + "pink2", + "pink3", + "pink4", + "plum", + "plum1", + "plum2", + "plum3", + "plum4", + "powderblue", + "purple", + "purple1", + "purple2", + "purple3", + "purple4", + "red", + "red1", + "red2", + "red3", + "red4", + "rosybrown", + "rosybrown1", + "rosybrown2", + "rosybrown3", + "rosybrown4", + "royalblue", + "royalblue1", + "royalblue2", + "royalblue3", + "royalblue4", + "saddlebrown", + "salmon", + "salmon1", + "salmon2", + "salmon3", + "salmon4", + "sandybrown", + "seagreen", + "seagreen1", + "seagreen2", + "seagreen3", + "seagreen4", + "seashell", + "seashell1", + "seashell2", + "seashell3", + "seashell4", + "sienna", + "sienna1", + "sienna2", + "sienna3", + "sienna4", + "skyblue", + "skyblue1", + "skyblue2", + "skyblue3", + "skyblue4", + "slateblue", + "slateblue1", + "slateblue2", + "slateblue3", + "slateblue4", + "slategray", + "slategray1", + "slategray2", + "slategray3", + "slategray4", + "slategrey", + "snow", + "snow1", + "snow2", + "snow3", + "snow4", + "springgreen", + "springgreen1", + "springgreen2", + "springgreen3", + "springgreen4", + "steelblue", + "steelblue1", + "steelblue2", + "steelblue3", + "steelblue4", + "tan", + "tan1", + "tan2", + "tan3", + "tan4", + "thistle", + "thistle1", + "thistle2", + "thistle3", + "thistle4", + "tomato", + "tomato1", + "tomato2", + "tomato3", + "tomato4", + "turquoise", + "turquoise1", + "turquoise2", + "turquoise3", + "turquoise4", + "violet", + "violetred", + "violetred1", + "violetred2", + "violetred3", + "violetred4", + "wheat", + "wheat1", + "wheat2", + "wheat3", + "wheat4", + "whitesmoke", + "yellow", + "yellow1", + "yellow2", + "yellow3", + "yellow4", + "yellowgreen" + ], + "defaultValue": "red", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Flip_Contrast", + "displayName": "Flip Contrast", + "description": "Select TRUE if you want to flip the contrast to opposite direction (flip the plot around the y-axis).", + "paramType": "BOOLEAN", + "paramGroup": "Plot", + "paramValues": null, + "defaultValue": "FALSE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Use_Default_X_Axis_Limit", + "displayName": "Use Default X-Axis Limit", + "description": "Use default x limit", + "paramType": "BOOLEAN", + "paramGroup": "Plot", + "paramValues": null, + "defaultValue": "TRUE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "X_Axis_Limit", + "displayName": "X-Axis Limit", + "description": "The limits of the x-axis (symmetric about 0)", + "paramType": "NUMBER", + "paramGroup": "Plot", + "paramValues": null, + "defaultValue": "5", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Use_Default_Y_Axis_Limit", + "displayName": "Use Default Y-Axis Limit", + "description": "Use Default Y limit", + "paramType": "BOOLEAN", + "paramGroup": "Plot", + "paramValues": null, + "defaultValue": "TRUE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Y_Axis_Limit", + "displayName": "Y-Axis Limit", + "description": "The upper limit of the y-axis", + "paramType": "NUMBER", + "paramGroup": "Plot", + "paramValues": null, + "defaultValue": "10", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Point_Size", + "displayName": "Point Size", + "description": "Size of a each data point", + "paramType": "STRING", + "paramGroup": "Plot", + "paramValues": null, + "defaultValue": "2", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "DEG_Columns_to_Keep_in_Output_Table", + "displayName": "DEG Columns to Keep in Output Table", + "description": "Select columns from input DEG results to include in the output dataset. If \"none\" is selected, then the output will contain only columns for Gene and Contrast.", + "paramType": "MULTISELECT", + "paramGroup": "Table", + "paramValues": [ + "FC", + "logFC", + "tstat", + "pval", + "adjpval", + "none" + ], + "defaultValue": "c(\"FC\",\"logFC\",\"tstat\",\"pval\",\"adjpval\")", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Image_Output_Format", + "displayName": "Image Output Format", + "description": "Select the image format for saved images: .png (default) .svg (vectorized)", + "paramType": "SELECT", + "paramGroup": "Image", + "paramValues": [ + "png", + "svg" + ], + "defaultValue": "png", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Use_svglite", + "displayName": "Use svglite", + "description": "If TRUE, generates the image using the svglite library, to enable easy editing using off-the-shelf SVG editors", + "paramType": "BOOLEAN", + "paramGroup": "Image", + "paramValues": null, + "defaultValue": "FALSE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Image_Width", + "displayName": "Image Width", + "description": "Image width in inches", + "paramType": "NUMBER", + "paramGroup": "Image", + "paramValues": null, + "defaultValue": "15", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Image_Height", + "displayName": "Image Height", + "description": "Image height in inches", + "paramType": "NUMBER", + "paramGroup": "Image", + "paramValues": null, + "defaultValue": "15", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Image_Resolution", + "displayName": "Image Resolution", + "description": "Image resolution in dpi (dots-per-inch) for png output", + "paramType": "NUMBER", + "paramGroup": "Image", + "paramValues": null, + "defaultValue": "300", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Use_Default_Grid_Layout", + "displayName": "Use Default Grid Layout", + "description": "if TRUE, an optimal number of rows in the figure grid layout is attempted; if you want to change the layout set the number of rows in the 'Number of rows in grid layout' parameter below", + "paramType": "BOOLEAN", + "paramGroup": "Image", + "paramValues": null, + "defaultValue": "TRUE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Number_of_Rows_in_Grid_Layout", + "displayName": "Number of Rows in Grid Layout", + "description": "", + "paramType": "NUMBER", + "paramGroup": "Image", + "paramValues": null, + "defaultValue": "1", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "Figure_Aspect_Ratio", + "displayName": "Figure Aspect Ratio", + "description": "figure aspect ratio, expressed as y / x; if 0, the ratio is based on the image size", + "paramType": "NUMBER", + "paramGroup": "Image", + "paramValues": null, + "defaultValue": "0", + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "title": "Volcano Plot - Summary [CCBR]", + "templateApiVersion": "0.1.0" +} \ No newline at end of file diff --git a/code/MOSuite/inst/extdata/galaxy/0_nidap-1.0/missing_parameters.csv b/code/MOSuite/inst/extdata/galaxy/0_nidap-1.0/missing_parameters.csv new file mode 100644 index 0000000..a8a9172 --- /dev/null +++ b/code/MOSuite/inst/extdata/galaxy/0_nidap-1.0/missing_parameters.csv @@ -0,0 +1,12 @@ +function_name,missing_arguments +batch_correct_counts,count_type;moo;plots_subdir;print_plots;save_plots;sub_count_type +clean_raw_counts,count_type;moo;print_plots;sample_id_colname;save_plots +diff_counts,count_type;moo;plots_subdir;print_plots;save_plots;sub_count_type +filter_counts,count_type;moo;number_of_histogram_legend_columns;plots_subdir;print_plots;save_plots +filter_diff,bar_width;draw_bar_border;fill_colors;label_distance;label_font_size;moo;pie_chart_in_3d;plot_titles_fontsize;plot_type;plots_subdir;print_plots;save_plots;y_axis_expansion +normalize_counts,count_type;moo;norm_type;plots_subdir;print_plots;save_plots +plot_expr_heatmap,color_values;group_colname;moo_counts;sample_metadata +plot_pca_3d,color_values;counts_dat;label_font_size;principal_components;sample_metadata +plot_venn_diagram,diff_summary_dat;dpi;graphics_device;image_height;image_width;plot_filename;plots_subdir;print_plots;save_plots +plot_volcano_enhanced,additional_labels;axis_lab_size;change_colname;change_lfc_name;change_sig_name;change_threshold;custom_xlim;dpi;image_height;image_width;interactive_plots;is_red;lab_size;moo_diff;num_features_to_label;plot_filename;plots_subdir;print_plots;save_plots;signif_colname;signif_threshold;title;use_custom_lab;use_only_addition_labels;value_to_sort_the_output_dataset;xlim_additional;ylim;ylim_additional +plot_volcano_summary,add_deg_columns;add_features;aspect_ratio;change_threshold;color_for_features_meeting_pvalue_and_foldchange_thresholds;color_of_features_meeting_only_signif_threshold;color_of_logfold_change_threshold_line;color_of_non_significant_features;color_of_signif_threshold_line;custom_gene_list;custom_gene_list_special_label_displacement;custom_label_color;default_label_color;displace_feature_labels;dpi;flip_vplot;graphics_device;image_height;image_width;label_features;label_x_adj;label_y_adj;line_thickness;moo_diff;num_features_to_label;plot_filename;plots_subdir;print_plots;save_plots;signif_colname;signif_threshold;value_to_sort_the_output_dataset diff --git a/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/batch_correct_counts.json b/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/batch_correct_counts.json new file mode 100644 index 0000000..77344a5 --- /dev/null +++ b/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/batch_correct_counts.json @@ -0,0 +1,167 @@ +{ + "title": "Batch Correction", + "description": "This template performs batch correction on RNA-seq expression data to account for batch effects that can arise whenever some samples are prepared in a different manner or at a different time than others. It takes a counts matrix (usually the normalized counts matrix) and your metadata table as input and provides two QC plots and a normalized expression matrix as output. This template is only necessary if your dataset has more than one batch. When necessary, it is usually the third step (after normalization) in the QC portion of a bulk RNA-seq analysis.\n\nBatch correction can only be attempted if your Batch variable is not completely confounded with your Group variable (see your metadata table). The two QC plots, a PCA plot and counts frequency histogram, are provided to help assess within and between group variance and the dis/similarity of sample count distributions, respectively.\n\nThe batch correction applied by this template is performed using the 'sva' R package's ComBat method.", + "r_function": "batch_correct_counts", + "columns": [ + { + "key": "feature_id_colname", + "displayName": "Feature ID Column", + "description": "The column from your input Counts Matrix containing the Feature IDs (Usually Gene or Protein ID). This is usually the first column of your input Counts Matrix. Only columns of Text type from your input Counts Matrix will be available to select for this parameter.", + "paramGroup": "Basic", + "sourceDataset": "counts_matrix", + "defaultValue": null, + "columnType": "STRING", + "isMulti": null + }, + { + "key": "samples_to_include", + "displayName": "Columns to Include", + "description": "Which Columns would you like to include? Usually, you will choose to \"Add all\" (see button on right). Columns excluded here will be removed in this step and from further analysis downstream of this step.", + "paramGroup": "Basic", + "sourceDataset": "counts_matrix", + "defaultValue": null, + "columnType": "ALL", + "isMulti": true + }, + { + "key": "sample_id_colname", + "displayName": "Sample Names Column", + "description": "The column from your input Sample Metadata table containing the sample names. The names in this column must exactly match the names used as the sample column names of your input Counts Matrix. Only columns of Text type from your input Sample Metadata table will be available to select for this parameter.", + "paramGroup": "Basic", + "sourceDataset": "sample_metadata", + "defaultValue": null, + "columnType": "STRING", + "isMulti": null + }, + { + "key": "covariates_colnames", + "displayName": "Covariates", + "description": "The column(s) from your input Sample Metadata table containing variable(s) of interest, such as phenotype. Most commonly this will be the same column you selected for your Groups Column (above). Some experimental designs may require that you add additional covariate columns here. \nNB. Do not include the \"Batch\" column here.", + "paramGroup": "Basic", + "sourceDataset": "sample_metadata", + "defaultValue": null, + "columnType": "ALL", + "isMulti": true + }, + { + "key": "batch_colname", + "displayName": "Batch Column", + "description": "The column from your input Sample Metadata table containing the batch information. Samples extracted, prepared, or sequenced at separate times or using separate materials/staff/equipment may belong to different batches. Not all datasets have batches. If yours dataset has no batches, you must still provide a Batch column with the same value in every row.", + "paramGroup": "Basic", + "sourceDataset": "sample_metadata", + "defaultValue": null, + "columnType": "ALL", + "isMulti": null + }, + { + "key": "label_colname", + "displayName": "Labels Column", + "description": "The column from your input Sample Metadata table containing the sample labels as you wish them to appear in the plots produced by this template. This can be the same Sample Names Column (see above). However, you may desire different labels to display on your figure (e.g. shorter labels are sometimes preferred on plots). In that case, select the column with your preferred Labels here.", + "paramGroup": "Basic", + "sourceDataset": "sample_metadata", + "defaultValue": null, + "columnType": "ALL", + "isMulti": null + } + ], + "inputDatasets": [ + { + "key": "moo_input_rds", + "displayName": "MOO input Rds", + "description": "File path to read the input multiOmicDataSet object (MOO)", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "parameters": [ + { + "key": "moo_output_rds", + "displayName": "MOO output Rds", + "description": "File path to output the multiOmicDataSet object (MOO) as an Rds file at the end of the function", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "count_type", + "displayName": "Count Type", + "description": "", + "paramType": "STRING", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": "raw", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "sub_count_type", + "displayName": "Sub Count Type", + "description": "", + "paramType": "STRING", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": "raw", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "colors_for_plots", + "displayName": "Colors for plots", + "description": "Colors for the PCA and histogram will be picked, in order, from this list. If more colors are needed, program will choose from a wide range of random colors", + "paramType": "MULTISELECT", + "paramGroup": "Visualization", + "paramValues": [ + "#5954d6", + "#e1562c", + "#b80058", + "#00c6f8", + "#d163e6", + "#00a76c", + "#ff9287", + "#008cf9", + "#006e00", + "#796880", + "#FFA500", + "#878500" + ], + "defaultValue": null, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "save_plots", + "displayName": "Save Plots", + "description": "If this is `TRUE`, any plots generated during the analysis will be saved to disk.", + "paramType": "BOOLEAN", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "outputDatasetName": "Batch-corrected MultiOmics Dataset", + "outputs": { + "multiOmicDataSet": { + "type": "file", + "name": "moo.rds" + }, + "figures": { + "type": "directory", + "name": "figures/batch/" + } + } +} \ No newline at end of file diff --git a/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/clean_raw_counts.json b/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/clean_raw_counts.json new file mode 100644 index 0000000..cbadece --- /dev/null +++ b/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/clean_raw_counts.json @@ -0,0 +1,159 @@ +{ + "title": "Clean Raw Counts", + "description": "This template checks the input raw counts matrix for common formatting problems with Feature identifiers (Gene or Peptide/Protein Names) and sample names. \n\nIf Feature IDs contain multiple IDs separated by special Characters((| - , or space) they will be split into multiple columns. \n\nIf Duplicate Feature ID's are detected the counts are summed across duplicate Feature ID rows within each sample.\n\nInvalid sample names will also be reported in the template Log and can be automatically corrected. If your sample names are corrected here, be sure to make equivalent changes to your metadata table.", + "r_function": "clean_raw_counts", + "columns": [ + { + "key": "feature_id_colname", + "displayName": "Feature ID Column", + "description": "Select a column from your counts that contains Feature IDs for each row. Defaults to the first column in the counts data.", + "paramGroup": "Basic", + "sourceDataset": "moo@counts", + "defaultValue": null, + "columnType": "STRING", + "isMulti": null + }, + { + "key": "sample_id_colname", + "displayName": "Sample ID Column", + "description": "Select a column from your sample metadata that contains Sample IDs for each column. Defaults to the first column in the sample metadata.", + "paramGroup": "Basic", + "sourceDataset": "moo@sample_meta", + "defaultValue": null, + "columnType": "STRING", + "isMulti": null + } + ], + "inputDatasets": [ + { + "key": "moo_input_rds", + "displayName": "MOO input Rds", + "description": "File path to read the input multiOmicDataSet object (MOO)", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "parameters": [ + { + "key": "moo_output_rds", + "displayName": "MOO output Rds", + "description": "File path to output the multiOmicDataSet object (MOO) as an Rds file at the end of the function", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "count_type", + "displayName": "Count Type", + "description": "", + "paramType": "STRING", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": "raw", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "samples_to_rename", + "displayName": "Samples to Rename", + "description": "Enter each sample that you want to rename in the format:\n\nold_name: new_name", + "paramType": "VECTOR", + "paramGroup": "Advanced", + "paramValues": null, + "defaultValue": "c(\"\")", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "cleanup_column_names", + "displayName": "Cleanup Column Names", + "description": "Invalid raw counts column names can cause errors in the downstream analysis. If this toggle is ON, any invalid column names will be automatically altered to a correct format.\n\nThese format changes will include adding an \"X\" as the first character in any column name that began with a numeral and replacing some special characters (\"-,:. \") with underscores (\"_\"). Invalid sample names and any changes made will be detailed in the template log.", + "paramType": "BOOLEAN", + "paramGroup": "Advanced", + "paramValues": null, + "defaultValue": "TRUE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "split_gene_name", + "displayName": "Split Feature ID", + "description": "", + "paramType": "BOOLEAN", + "paramGroup": "Advanced", + "paramValues": null, + "defaultValue": "TRUE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "aggregate_rows_with_duplicate_gene_names", + "displayName": "Aggregate Rows with Duplicate Feature Names", + "description": "Regardless of the toggle status (ON/OFF), if a Feature ID (from the \"Cleanup Column Names\" parameter above) is found to be duplicated on multiple rows of the raw counts, the Log will report these Feature IDs.\n\nUsing the default behavior (ON), the counts for all rows with a duplicate Feature IDs are aggregated into a single row. Counts are summed across duplicate Feature ID rows within each sample. Additional identifier columns, if present (e.g. Ensembl IDs), will be preserved and multiple matching identifiers in such additional columns will appear as comma-separated values in an aggregated row.", + "paramType": "BOOLEAN", + "paramGroup": "Advanced", + "paramValues": null, + "defaultValue": "TRUE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "gene_name_column_to_use_for_collapsing_duplicates", + "displayName": "Column Used to Aggregate Duplicates Feature IDs", + "description": "Select the column with Feature IDs to use as grouping elements to collapse the counts matrix.\n\nThe log output will list the columns available to identify duplicate row IDs in order to aggregate information. \n\nIf Bulk RNAseq data your column selected for Feature ID will be renamed to \"Gene\" \nIf analyzing Proteomics data your column selected for Feature ID will be renamed to \"Feature ID\".\n\nIf left blank your \"Feature ID\" Column will be used to Aggregate Rows.\n\nIf \"Feature ID\" column can be split into multiple IDs the non Ensembl ID name will be used to aggregate duplicate IDs.\nIf \"Feature ID\" column does not contain Ensembl IDs the split Feature IDs will be named 'Feature_id_1' and 'Feature_id_2'. For this case the Template will error out and you will have to manually enter Column ID for this field.", + "paramType": "STRING", + "paramGroup": "Advanced", + "paramValues": [ + "Gene", + "Pepetide", + "Protein", + "Ensembl_ID", + "Ensembl_ID_version", + "Gene_id_1", + "Gene_id_2", + "Original Gene Column" + ], + "defaultValue": "", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "save_plots", + "displayName": "Save Plots", + "description": "If this is `TRUE`, any plots generated during the analysis will be saved to disk.", + "paramType": "BOOLEAN", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "outputDatasetName": "Cleaned MultiOmics Dataset", + "outputs": { + "multiOmicDataSet": { + "type": "file", + "name": "moo.rds" + }, + "figures": { + "type": "directory", + "name": "figures/clean/" + } + } +} diff --git a/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/create_multiOmicDataSet_from_files.json b/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/create_multiOmicDataSet_from_files.json new file mode 100644 index 0000000..54d8019 --- /dev/null +++ b/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/create_multiOmicDataSet_from_files.json @@ -0,0 +1,89 @@ +{ + "title": "Create Multi-Omic Dataset from Files", + "description": "", + "r_function": "create_multiOmicDataSet_from_files", + "columns": [], + "inputDatasets": [ + { + "key": "sample_meta_filepath", + "displayName": "", + "description": "", + "paramType": "TABULAR", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": null, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "feature_counts_filepath", + "displayName": "", + "description": "", + "paramType": "TABULAR", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": null, + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "parameters": [ + { + "key": "moo_output_rds", + "displayName": "MOO output Rds", + "description": "File path to output the multiOmicDataSet object (MOO) as an Rds file", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "sample_id_colname", + "displayName": "", + "description": "", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": null, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "feature_id_colname", + "displayName": "", + "description": "", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": null, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "delim", + "displayName": "", + "description": "", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": null, + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "outputDatasetName": "MultiOmics Dataset", + "outputs": { + "multiOmicDataSet": { + "type": "file", + "name": "moo.rds" + } + } +} \ No newline at end of file diff --git a/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/diff_counts.json b/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/diff_counts.json new file mode 100644 index 0000000..87394f2 --- /dev/null +++ b/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/diff_counts.json @@ -0,0 +1,189 @@ +{ + "title": "Differential Analysis", + "description": "Performs Differential Expression of Genes (DEG) Analysis.\n\nThis template takes (filtered) raw counts as its input and transforms this count data to log2-counts per million (logCPM). The normalization and DEG analysis is implemented using the Limma Voom R package.\n\nThe returned counts matrix contains normalized counts, not batch corrected counts. The DEG analysis accounts for batch using covariates, however. You can optionally also return mean and standard deviation of normalized expression within groups.\n\nThis template will support up to 2 factors", + "r_function": "diff_counts", + "columns": [ + { + "key": "feature_id_colname", + "displayName": "Feature/Gene Names Column", + "description": "The column from your counts matrix containing the Feature ID (gene names).", + "paramGroup": "Basic", + "sourceDataset": "Counts_Matrix", + "defaultValue": null, + "columnType": "STRING", + "isMulti": null + }, + { + "key": "sample_id_colname", + "displayName": "Sample Names Column", + "description": "Column containing sample names", + "paramGroup": "Basic", + "sourceDataset": "Sample_Metadata", + "defaultValue": null, + "columnType": "ALL", + "isMulti": null + }, + { + "key": "samples_to_include", + "displayName": "Columns to Include", + "description": "Select the sample columns from the input counts matrix that you want to process. Only numeric columns can be selected.", + "paramGroup": "Basic", + "sourceDataset": "Counts_Matrix", + "defaultValue": null, + "columnType": "ALL", + "isMulti": true + }, + { + "key": "contrast_colname", + "displayName": "Contrast Variable Column", + "description": "The column in the input Sample Metadata that contains the group variables you wish to find differential expression between. User can add up to 2 columns (2-factor analysis)", + "paramGroup": "Basic", + "sourceDataset": "Sample_Metadata", + "defaultValue": null, + "columnType": "ALL", + "isMulti": true + }, + { + "key": "covariates_colnames", + "displayName": "Covariates Column(s)", + "description": "Columns to be used as covariates in linear modeling. Must include column from \"Contrast Variable\". Most commonly your covariate will be group and batch (if you have different batches in your data).", + "paramGroup": "Basic", + "sourceDataset": "Sample_Metadata", + "defaultValue": null, + "columnType": "ALL", + "isMulti": true + } + ], + "inputDatasets": [ + { + "key": "moo_input_rds", + "displayName": "MOO input Rds", + "description": "File path to read the input multiOmicDataSet object (MOO)", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "parameters": [ + { + "key": "moo_output_rds", + "displayName": "MOO output Rds", + "description": "File path to output the multiOmicDataSet object (MOO) as an Rds file at the end of the function", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "count_type", + "displayName": "Count Type", + "description": "", + "paramType": "STRING", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": "raw", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "sub_count_type", + "displayName": "Sub Count Type", + "description": "", + "paramType": "STRING", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": "raw", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "contrasts", + "displayName": "Contrasts", + "description": "Specify each contrast in the format group1-group2, e.g. treated-control", + "paramType": "VECTOR", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": null, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "input_in_log_counts", + "displayName": "Input in log Counts", + "description": "Set to TRUE if input is in log counts.", + "paramType": "BOOLEAN", + "paramGroup": "Advanced", + "paramValues": null, + "defaultValue": "FALSE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "return_mean_and_sd", + "displayName": "Return Mean and SD", + "description": "if TRUE, return Mean and Standard Deviation of groups in addition to DEG estimates for contrast(s)", + "paramType": "BOOLEAN", + "paramGroup": "Advanced", + "paramValues": null, + "defaultValue": "FALSE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "voom_normalization_method", + "displayName": "Normalization Method", + "description": "Normalization method to be applied to the logCPM values", + "paramType": "SELECT", + "paramGroup": "Advanced", + "paramValues": [ + "none", + "scale", + "quantile", + "cyclicloess", + "TMM", + "TMMwzp", + "RLE", + "upperquartile" + ], + "defaultValue": "quantile", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "save_plots", + "displayName": "Save Plots", + "description": "If this is `TRUE`, any plots generated during the analysis will be saved to disk.", + "paramType": "BOOLEAN", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "outputDatasetName": "Differential Counts from MultiOmics Dataset", + "outputs": { + "multiOmicDataSet": { + "type": "file", + "name": "moo.rds" + }, + "figures": { + "type": "directory", + "name": "figures/diff/" + } + } +} \ No newline at end of file diff --git a/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/filter_counts.json b/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/filter_counts.json new file mode 100644 index 0000000..f2eca99 --- /dev/null +++ b/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/filter_counts.json @@ -0,0 +1,433 @@ +{ + "title": "Filter Low Counts", + "description": "This template is intended for use with Bulk RNA-seq data and is often the first step in the QC portion of an analysis. It filters out Features that have very low raw counts across most or all of your samples.\n\nThis template takes as input a raw counts expression matrix and your sample metadata table. It provides as output an image consisting of three QC plots (see below) and a filtered raw counts expression matrix. You have an option to use CPM counts as input instead.\n\nThe threshold for tuning how low counts for a given gene are before they are deemed \"too low\" and filtered out of downstream analysis is a tunable parameter. By default, this parameter is set to 1, meaning any raw count value less than 1 will count as \"too low\".\n\nThe QC plots are provided to help you assess: (1) PCA Plot: the within and between group variance in expression after dimensionality reduction; (2) Count Density Histogram: the dis/similarity of count distributions between samples; and (3) Similarity Heatmap: the overall similarity of samples to one another based on unsupervised clustering.", + "r_function": "filter_counts", + "columns": [ + { + "key": "feature_id_colname", + "displayName": "Feature ID Column", + "description": "The column from your input Counts Matrix containing the Feature IDs (Usually Gene or Protein ID). This is usually the first column of your input Counts Matrix. Only columns of Text type from your input Counts Matrix will be available to select for this parameter.", + "paramGroup": "Basic", + "sourceDataset": "counts_matrix", + "defaultValue": null, + "columnType": "STRING", + "isMulti": null + }, + { + "key": "samples_to_include", + "displayName": "Columns to Include", + "description": "Which Columns would you like to include? Usually, you will choose to \"Add all\" (see button on right). Columns excluded here will be removed in this step and from further analysis downstream of this step.", + "paramGroup": "Basic", + "sourceDataset": "counts_matrix", + "defaultValue": null, + "columnType": "ALL", + "isMulti": true + }, + { + "key": "sample_id_colname", + "displayName": "Sample Names Column", + "description": "The column from your input Sample Metadata table containing the sample names. The names in this column must exactly match the names used as the sample column names of your input Counts Matrix. Only columns of Text type from your input Sample Metadata table will be available to select for this parameter.", + "paramGroup": "Basic", + "sourceDataset": "Sample_Metadata", + "defaultValue": null, + "columnType": "STRING", + "isMulti": null + }, + { + "key": "group_colname", + "displayName": "Groups Column", + "description": "The column from your input Sample Metadata table containing the sample group information. This is usually a column showing to which experimental treatments each sample belongs (e.g. WildType, Knockout, Tumor, Normal, Before, After, etc.). Only columns of Text type from your input Sample Metadata will be available to select for this parameter.", + "paramGroup": "Basic", + "sourceDataset": "Sample_Metadata", + "defaultValue": null, + "columnType": "STRING", + "isMulti": null + }, + { + "key": "label_colname", + "displayName": "Labels Column", + "description": "The column from your input Sample Metadata table containing the sample labels as you wish them to appear in the plots produced by this template. This can be the same Sample Names Column (see above). However, you may desire different labels to display on your figure (e.g. shorter labels are sometimes preferred on plots). In that case, select the column with your preferred Labels here. The selected column should contain unique names for each sample.", + "paramGroup": "Basic", + "sourceDataset": "Sample_Metadata", + "defaultValue": null, + "columnType": "ALL", + "isMulti": null + } + ], + "inputDatasets": [ + { + "key": "moo_input_rds", + "displayName": "MOO input Rds", + "description": "File path to read the input multiOmicDataSet object (MOO)", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "parameters": [ + { + "key": "moo_output_rds", + "displayName": "MOO output Rds", + "description": "File path to output the multiOmicDataSet object (MOO) as an Rds file at the end of the function", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "count_type", + "displayName": "Count Type", + "description": "", + "paramType": "STRING", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": "raw", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "use_cpm_counts_to_filter", + "displayName": "Use CPM Counts to filter", + "description": "If no transformation has been been performed on counts matrix (eg Raw Counts) set to TRUE. If TRUE counts will be transformed to CPM and filtered based on given criteria.\n If gene counts matrix has been transformed (eg log2, CPM, FPKM or some form of Normalization) set to FALSE. If FALSE no further transformation will be applied and features will be filtered as is. For RNAseq data RAW counts should be transformed to CPM in order to properly filter.", + "paramType": "BOOLEAN", + "paramGroup": "Filtering", + "paramValues": null, + "defaultValue": "TRUE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "minimum_count_value_to_be_considered_nonzero", + "displayName": "Minimum Count Value to be Considered Nonzero", + "description": "", + "paramType": "NUMBER", + "paramGroup": "Filtering", + "paramValues": null, + "defaultValue": "1", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "minimum_number_of_samples_with_nonzero_counts_in_total", + "displayName": "Minimum Number of Samples with Nonzero Counts in Total", + "description": "Minimum number of samples (total) with non-zero counts", + "paramType": "NUMBER", + "paramGroup": "Filtering", + "paramValues": null, + "defaultValue": "1", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "use_group_based_filtering", + "displayName": "Use Group-Based Filtering", + "description": "If TRUE, only keeps genes that have at least a certain number of samples with nonzero CPM counts in at least one group", + "paramType": "BOOLEAN", + "paramGroup": "Filtering", + "paramValues": null, + "defaultValue": "TRUE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "minimum_number_of_samples_with_nonzero_counts_in_a_group", + "displayName": "Minimum Number of Samples with Nonzero Counts in a Group", + "description": "Only keeps genes that have at least this number of samples with nonzero CPM counts in at least one group", + "paramType": "NUMBER", + "paramGroup": "Filtering", + "paramValues": null, + "defaultValue": "3", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "principal_component_on_x_axis", + "displayName": "Principal Component on X-axis", + "description": "The principle component to plot on the x-axis. Choices include 1, 2, 3, ... (default: 1)", + "paramType": "NUMBER", + "paramGroup": "PCA", + "paramValues": null, + "defaultValue": "1", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "principal_component_on_y_axis", + "displayName": "Principal Component on Y-axis", + "description": "The principle component to plot on the y-axis. Choices include 1, 2, 3, ... (default: 2)", + "paramType": "NUMBER", + "paramGroup": "PCA", + "paramValues": null, + "defaultValue": "2", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "legend_position_for_pca", + "displayName": "Legend Position for PCA", + "description": "Legend position relative to the plot", + "paramType": "SELECT", + "paramGroup": "PCA", + "paramValues": [ + "top", + "bottom", + "left", + "right", + "none" + ], + "defaultValue": "top", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "point_size_for_pca", + "displayName": "Point Size for PCA", + "description": "", + "paramType": "NUMBER", + "paramGroup": "PCA", + "paramValues": null, + "defaultValue": "1", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "add_label_to_pca", + "displayName": "Add Labels to PCA", + "description": "Label points on graph", + "paramType": "BOOLEAN", + "paramGroup": "PCA", + "paramValues": null, + "defaultValue": "TRUE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "label_font_size", + "displayName": "Label Font Size for PCA", + "description": "Font size for sample labels. Set to 0 to remove labels.", + "paramType": "NUMBER", + "paramGroup": "PCA", + "paramValues": null, + "defaultValue": "3", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "label_offset_x_", + "displayName": "Label Offset (x)", + "description": "", + "paramType": "NUMBER", + "paramGroup": "PCA", + "paramValues": null, + "defaultValue": "2", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "label_offset_y_", + "displayName": "Label Offset (Y)", + "description": "", + "paramType": "NUMBER", + "paramGroup": "PCA", + "paramValues": null, + "defaultValue": "2", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "samples_to_rename", + "displayName": "Samples to Rename Manually on PCA", + "description": "If you do not have a Plot Labels Column (see above) in your sample metadata table, you can use this parameter to rename samples manually for display on the PCA plot. Use \"Add item\" to add each additional sample for renaming. Use the following format to describe which old name (in your sample metadata table) you want to rename to which new name: old_name: new_name", + "paramType": "VECTOR", + "paramGroup": "PCA", + "paramValues": null, + "defaultValue": "c(\"\")", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "color_histogram_by_group", + "displayName": "Color Histogram by Group", + "description": "Toggle to FALSE to label histogram by Sample Names. Toggle to TRUE to label histogram by the column you select in the \"Group Column Used to Color Histogram\" parameter (below). Default is FALSE.", + "paramType": "BOOLEAN", + "paramGroup": "Histogram", + "paramValues": null, + "defaultValue": "FALSE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "set_min_max_for_x_axis_for_histogram", + "displayName": "Set Min/Max for X-axis for Histogram", + "description": "", + "paramType": "BOOLEAN", + "paramGroup": "Histogram", + "paramValues": null, + "defaultValue": "FALSE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "minimum_for_x_axis_for_histogram", + "displayName": "Minimum for X-axis for Histogram", + "description": "", + "paramType": "NUMBER", + "paramGroup": "Histogram", + "paramValues": null, + "defaultValue": "-1", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "maximum_for_x_axis_for_histogram", + "displayName": "Maximum for X-axis for Histogram", + "description": "", + "paramType": "NUMBER", + "paramGroup": "Histogram", + "paramValues": null, + "defaultValue": "1", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "legend_font_size_for_histogram", + "displayName": "Legend Font Size for Histogram", + "description": "Legend font size", + "paramType": "NUMBER", + "paramGroup": "Histogram", + "paramValues": null, + "defaultValue": "10", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "legend_position_for_histogram", + "displayName": "Legend Position for Histogram", + "description": "Legend position on histogram plot, can be 'none' if large number of samples", + "paramType": "SELECT", + "paramGroup": "Histogram", + "paramValues": [ + "right", + "bottom", + "left", + "top", + "none" + ], + "defaultValue": "top", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "number_of_histogram_legend_columns", + "displayName": "Number of Histogram Legend Columns", + "description": "", + "paramType": "NUMBER", + "paramGroup": "Histogram", + "paramValues": null, + "defaultValue": "6", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "colors_for_plots", + "displayName": "Colors for Plots", + "description": "Colors for the PCA and histogram will be picked, in order, from this list. If you have >12 samples or groups, program will choose from a wide range of random colors", + "paramType": "MULTISELECT", + "paramGroup": "Visualization", + "paramValues": [ + "#5954d6", + "#e1562c", + "#b80058", + "#00c6f8", + "#d163e6", + "#00a76c", + "#ff9287", + "#008cf9", + "#006e00", + "#796880", + "#FFA500", + "#878500" + ], + "defaultValue": null, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "interactive_plots", + "displayName": "Interactive Plots", + "description": "Toggle TRUE to make PCA and Histogram plots interactive, allowing you to hover your mouse over a point or line to view sample information. The similarity heatmap will not display if this toggle is set to TRUE. Default is FALSE.", + "paramType": "BOOLEAN", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": "FALSE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "plot_corr_matrix_heatmap", + "displayName": "Plot Correlation Matrix Heatmap", + "description": "Datasets with a large number of samples may be too large to create a correlation matix heatmap. If this template takes longer than 5 minutes to run, Toggle switch to FALSE and the correlation matrix will not be be created. Default is TRUE.", + "paramType": "BOOLEAN", + "paramGroup": "TCGA", + "paramValues": null, + "defaultValue": "TRUE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "save_plots", + "displayName": "Save Plots", + "description": "If this is `TRUE`, any plots generated during the analysis will be saved to disk.", + "paramType": "BOOLEAN", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "outputDatasetName": "Filtered MultiOmics Dataset", + "outputs": { + "multiOmicDataSet": { + "type": "file", + "name": "moo.rds" + }, + "figures": { + "type": "directory", + "name": "figures/filt/" + } + } +} \ No newline at end of file diff --git a/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/filter_diff.json b/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/filter_diff.json new file mode 100644 index 0000000..21bc470 --- /dev/null +++ b/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/filter_diff.json @@ -0,0 +1,357 @@ +{ + "title": "Filter Differential Features", + "description": "Outputs dataset of significant genes from DEG table; filters genes based on statistical significance (p-value or adjusted p-value) and change (fold change, log2 fold change, or t-statistic); in addition allows for selection of DEG estimates and for sub-setting of contrasts and groups included in the output gene list.", + "r_function": "filter_diff", + "columns": [ + { + "key": "feature_id_colname", + "displayName": "Gene Names Column", + "description": "The column from your input DEG Table containing the gene names. This is usually the first column of your input DEG Table. Only columns of Text type from your input DEG Table will be available to select for this parameter.", + "paramGroup": "Basic", + "sourceDataset": "DEG_Table", + "defaultValue": null, + "columnType": "STRING", + "isMulti": null + } + ], + "inputDatasets": [ + { + "key": "moo_input_rds", + "displayName": "MOO input Rds", + "description": "File path to read the input multiOmicDataSet object (MOO)", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "parameters": [ + { + "key": "moo_output_rds", + "displayName": "MOO output Rds", + "description": "File path to output the multiOmicDataSet object (MOO) as an Rds file at the end of the function", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "significance_column", + "displayName": "Significance Column", + "description": "", + "paramType": "SELECT", + "paramGroup": "Basic", + "paramValues": [ + "adjpval", + "pval" + ], + "defaultValue": "adjpval", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "significance_cutoff", + "displayName": "Significance Cutoff", + "description": "", + "paramType": "NUMBER", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": "0.01", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "change_column", + "displayName": "Change Column", + "description": "", + "paramType": "SELECT", + "paramGroup": "Basic", + "paramValues": [ + "FC", + "logFC", + "tstat" + ], + "defaultValue": "logFC", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "change_cutoff", + "displayName": "Change Cutoff", + "description": "Absolute value of the cutoff; default cutoff set to 1 in log2 scale (2-fold change)", + "paramType": "NUMBER", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": "1", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "filtering_mode", + "displayName": "Filtering Mode", + "description": "", + "paramType": "SELECT", + "paramGroup": "Basic", + "paramValues": [ + "any", + "all" + ], + "defaultValue": "any", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "include_estimates", + "displayName": "Include Estimates", + "description": "", + "paramType": "MULTISELECT", + "paramGroup": "Advanced", + "paramValues": [ + "mean", + "sd", + "FC", + "logFC", + "tstat", + "pval", + "adjpval" + ], + "defaultValue": [ + "mean", + "sd", + "FC", + "logFC", + "tstat", + "pval", + "adjpval" + ], + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "round_estimates", + "displayName": "Round Estimates", + "description": "", + "paramType": "BOOLEAN", + "paramGroup": "Advanced", + "paramValues": null, + "defaultValue": "TRUE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "contrast_filter", + "displayName": "Contrasts Filter", + "description": "", + "paramType": "SELECT", + "paramGroup": "Filter", + "paramValues": [ + "none", + "keep", + "remove" + ], + "defaultValue": "none", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "contrasts", + "displayName": "Contrasts", + "description": "", + "paramType": "VECTOR", + "paramGroup": "Filter", + "paramValues": null, + "defaultValue": "c()", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "groups_filter", + "displayName": "Groups Filter", + "description": "", + "paramType": "SELECT", + "paramGroup": "Filter", + "paramValues": [ + "none", + "keep", + "remove" + ], + "defaultValue": "none", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "groups", + "displayName": "Groups", + "description": "", + "paramType": "VECTOR", + "paramGroup": "Filter", + "paramValues": null, + "defaultValue": "c()", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "label_font_size", + "displayName": "Label Font Size", + "description": "", + "paramType": "NUMBER", + "paramGroup": "Label", + "paramValues": null, + "defaultValue": "6", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "label_distance", + "displayName": "Label Distance", + "description": "Distance of text label from top of a bar", + "paramType": "NUMBER", + "paramGroup": "Label", + "paramValues": null, + "defaultValue": "1", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "y_axis_expansion", + "displayName": "Y-Axis Expansion", + "description": "multiplicative expansion of y-axis limits; increase/decrease this number if the text label above the bar requires more/less space", + "paramType": "NUMBER", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": "0.08", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "fill_colors", + "displayName": "Fill Colors ", + "description": "", + "paramType": "MULTISELECT", + "paramGroup": "Visualization", + "paramValues": [ + "aliceblue", + "antiquewhite4", + "darkorange", + "gold", + "red3", + "springgreen", + "steelblue1", + "blue2", + "violetred3", + "whitesmoke", + "gray60", + "gray90", + "black", + "white" + ], + "defaultValue": "c(\"steelblue1\",\"whitesmoke\")", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "pie_chart_in_3d", + "displayName": "Pie Chart in 3D", + "description": "If TRUE, a 3D Pie chart is plotted with 'Filtering mode' set to 'in all contrasts', if FALSE, a 2D chart will be plotted for this filtering mode.", + "paramType": "BOOLEAN", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": "TRUE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "bar_width", + "displayName": "Bar Width", + "description": "Bar width in the bar chart plotted with Filtering mode set to 'in any contrast'", + "paramType": "NUMBER", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": "0.4", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "draw_bar_border", + "displayName": "Draw Bar Border", + "description": "", + "paramType": "BOOLEAN", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": "TRUE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "rounding_decimal_for_percent_cells", + "displayName": "Rounding Decimal for Percent Calls", + "description": "applies to display of percent significant and non-significant calls", + "paramType": "NUMBER", + "paramGroup": "Advanced", + "paramValues": null, + "defaultValue": "0", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "plot_titles_fontsize", + "displayName": "Font Size for Plot Titles", + "description": "", + "paramType": "NUMBER", + "paramGroup": "Label", + "paramValues": null, + "defaultValue": 12, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "save_plots", + "displayName": "Save Plots", + "description": "If this is `TRUE`, any plots generated during the analysis will be saved to disk.", + "paramType": "BOOLEAN", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "outputDatasetName": "Filtered Differential Counts from MultiOmics Dataset", + "outputs": { + "multiOmicDataSet": { + "type": "file", + "name": "moo.rds" + }, + "figures": { + "type": "directory", + "name": "figures/diff/filt/" + } + } +} \ No newline at end of file diff --git a/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/initialize-templates.py b/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/initialize-templates.py new file mode 100644 index 0000000..cc899c7 --- /dev/null +++ b/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/initialize-templates.py @@ -0,0 +1,57 @@ +#!/usr/bin/env python + +import json +import glob +import pathlib + + +def main(): + with open( + "inst/extdata/galaxy/0_nidap-1.0/NIDAPBulkTemplate_parameterTo_MOSuiteMapping.json", + "r", + ) as infile: + template_mappings = json.load(infile)["template_mappings"] + for filename in glob.glob("inst/extdata/galaxy/0_nidap-1.0/*.code-template.json"): + code_template_file = pathlib.Path(filename) + with open(code_template_file, "r") as infile: + code_template = json.load(infile) + template_name = code_template_file.name + mapping = next( + ( + meta + for key, meta in template_mappings.items() + if key == template_name + ), + {}, + ) + new_template = { + "title": code_template["title"].replace(" [CCBR]", ""), + "description": code_template["description"], + "r_function": mapping.get("r_function", ""), + "columns": [], + "inputDatasets": [], + "parameters": [], + } + for arg_type in ("columns", "inputDatasets", "parameters"): + for param in code_template.get(arg_type, []): + param_name = param.get("key") + params_lst = mapping.get("parameter_mappings", []) + new_param = next( + (p.get(param_name) for p in params_lst if param_name in p), None + ) + if new_param: + param["key"] = new_param + new_template[arg_type].append(param) + else: + new_template[arg_type].append(param) + with open( + pathlib.Path( + f"inst/extdata/galaxy/1_mosuite-templates/{new_template['r_function']}.json" + ), + "w", + ) as outfile: + json.dump(new_template, outfile, indent=4) + + +if __name__ == "__main__": + main() diff --git a/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/normalize_counts.json b/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/normalize_counts.json new file mode 100644 index 0000000..d6073e8 --- /dev/null +++ b/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/normalize_counts.json @@ -0,0 +1,414 @@ +{ + "title": "Normalization", + "description": "This template is intended for use with Bulk RNA-seq data and is often performed immediately after filtering for low count genes. It normalizes RNA-seq expression data to account for factors that would prevent direct comparisons between samples.\n\nThis template takes as input a counts matrix (usually the filtered counts matrix) and your sample metadata table. It provides as output an image consisting of three QC plots (see below) and a normalized expression matrix.\n\nThe default normalization method is quantile, which is a very common way to normalize bulk RNA-seq data. Other normalization methods are selectable, as needed.\n\nThe QC plots provided are: (1) PCA Plot: shows the within- and between-group variance in expression after dimensionality reduction; (2) Count Density Histogram: shows the dis/similarity of count distributions between samples; and (3) Similarity Heatmap: shows the overall similarity of samples to one another based on unsupervised clustering.", + "r_function": "normalize_counts", + "columns": [ + { + "key": "feature_id_colname", + "displayName": "Feature ID Column", + "description": "The column from your input Counts Matrix containing the Feature IDs (Usually Gene or Protein ID). This is usually the first column of your input Counts Matrix. Only columns of Text type from your input Counts Matrix will be available to select for this parameter.", + "paramGroup": "Basic", + "sourceDataset": "counts_matrix", + "defaultValue": null, + "columnType": "STRING", + "isMulti": null + }, + { + "key": "samples_to_include", + "displayName": "Columns to Include", + "description": "Which Columns would you like to include? Usually, you will choose to \"Add all\" (see button on right). Columns excluded here will be removed in this step and from further analysis downstream of this step.", + "paramGroup": "Basic", + "sourceDataset": "counts_matrix", + "defaultValue": null, + "columnType": "ALL", + "isMulti": true + }, + { + "key": "sample_id_colname", + "displayName": "Sample Names Column", + "description": "The column from your input Sample Metadata table containing the sample names. The names in this column must exactly match the names used as the sample column names of your input Counts Matrix. Only columns of Text type from your input Sample Metadata table will be available to select for this parameter.", + "paramGroup": "Basic", + "sourceDataset": "Sample_Metadata", + "defaultValue": null, + "columnType": "STRING", + "isMulti": null + }, + { + "key": "group_colname", + "displayName": "Groups Column", + "description": "The column from your input Sample Metadata table containing the sample group information. This is usually a column showing to which experimental treatments each sample belongs (e.g. WildType, Knockout, Tumor, Normal, Before, After, etc.). Only columns of Text type from your input Sample Metadata will be available to select for this parameter.", + "paramGroup": "Basic", + "sourceDataset": "Sample_Metadata", + "defaultValue": null, + "columnType": "ALL", + "isMulti": null + }, + { + "key": "label_colname", + "displayName": "Labels Column", + "description": "The column from your input Sample Metadata table containing the sample labels as you wish them to appear in the plots produced by this template. This can be the same Sample Names Column (see above). However, you may desire different labels to display on your figure (e.g. shorter labels are sometimes preferred on plots). In that case, select the column with your preferred Labels here.", + "paramGroup": "Basic", + "sourceDataset": "Sample_Metadata", + "defaultValue": null, + "columnType": "ALL", + "isMulti": null + } + ], + "inputDatasets": [ + { + "key": "moo_input_rds", + "displayName": "MOO input Rds", + "description": "File path to read the input multiOmicDataSet object (MOO)", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "parameters": [ + { + "key": "moo_output_rds", + "displayName": "MOO output Rds", + "description": "File path to output the multiOmicDataSet object (MOO) as an Rds file at the end of the function", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "count_type", + "displayName": "Count Type", + "description": "", + "paramType": "STRING", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": "raw", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "norm_type", + "displayName": "Normalization Type", + "description": "", + "paramType": "STRING", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": "raw", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "input_in_log_counts", + "displayName": "Input in Log Counts", + "description": "TRUE if input is in log counts", + "paramType": "BOOLEAN", + "paramGroup": "Normalization", + "paramValues": null, + "defaultValue": "FALSE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "voom_normalization_method", + "displayName": "Normalization Method", + "description": "Normalization method to be applied to the logCPM values", + "paramType": "SELECT", + "paramGroup": "Normalization", + "paramValues": [ + "none", + "scale", + "quantile", + "cyclicloess" + ], + "defaultValue": "quantile", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "samples_to_rename", + "displayName": "Samples to Rename Manually on PCA", + "description": "Enter each sample to rename in the format: old_name: new_name", + "paramType": "VECTOR", + "paramGroup": "PCA", + "paramValues": null, + "defaultValue": "c(\"\")", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "add_label_to_pca", + "displayName": "Add Labels to PCA", + "description": "Toggle to TRUE to use the column from \"Label Column to Use for Plots\" (above) to label points on the PCA plot. Toggle to FALSE to remove these labels from the plot. Default is TRUE.", + "paramType": "BOOLEAN", + "paramGroup": "PCA", + "paramValues": null, + "defaultValue": "TRUE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "principal_component_on_x_axis", + "displayName": "Principal Component on X-axis for PCA", + "description": "The principle component to plot on the x-axis. Choices include 1, 2, 3, ... (default: 1)", + "paramType": "NUMBER", + "paramGroup": "PCA", + "paramValues": null, + "defaultValue": "1", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "principal_component_on_y_axis", + "displayName": "Principal Component on Y-axis for PCA", + "description": "The principle component to plot on the y-axis. Choices include 1, 2, 3, ... (default: 2)", + "paramType": "NUMBER", + "paramGroup": "PCA", + "paramValues": null, + "defaultValue": "2", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "legend_position_for_pca", + "displayName": "Legend position for PCA", + "description": "Legend position relative to the plot", + "paramType": "SELECT", + "paramGroup": "PCA", + "paramValues": [ + "top", + "bottom", + "left", + "right", + "none" + ], + "defaultValue": "top", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "label_offset_x_", + "displayName": "Label Offset (x) for PCA", + "description": "", + "paramType": "NUMBER", + "paramGroup": "PCA", + "paramValues": null, + "defaultValue": "2", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "label_offset_y_", + "displayName": "Label Offset (y) for PCA", + "description": "", + "paramType": "NUMBER", + "paramGroup": "PCA", + "paramValues": null, + "defaultValue": "2", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "label_font_size", + "displayName": "Label Font Size for PCA", + "description": "Font size for sample labels on the PCA. Set to 0 to remove labels.", + "paramType": "NUMBER", + "paramGroup": "PCA", + "paramValues": null, + "defaultValue": "3", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "point_size_for_pca", + "displayName": "Point Size for PCA", + "description": "Size of a each data point on the PCA.", + "paramType": "NUMBER", + "paramGroup": "PCA", + "paramValues": null, + "defaultValue": "2", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "color_histogram_by_group", + "displayName": "Color Histogram by Group", + "description": "Toggle to FALSE to label histogram by Sample Names. Toggle to TRUE to label histogram by the column you select in the \"Group Column Used to Color Histogram\" parameter (below). Default is FALSE.", + "paramType": "BOOLEAN", + "paramGroup": "Histogram", + "paramValues": null, + "defaultValue": "FALSE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "maximum_for_x_axis_for_histogram", + "displayName": "Maximum for X-axis in Histogram", + "description": "", + "paramType": "NUMBER", + "paramGroup": "Histogram", + "paramValues": null, + "defaultValue": "1", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "minimum_for_x_axis_for_histogram", + "displayName": "Minimum for X-axis in Histogram", + "description": "", + "paramType": "NUMBER", + "paramGroup": "Histogram", + "paramValues": null, + "defaultValue": "-1", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "set_min_max_for_x_axis_for_histogram", + "displayName": "Set Min/Max for X-axis for Histogram", + "description": "", + "paramType": "BOOLEAN", + "paramGroup": "Histogram", + "paramValues": null, + "defaultValue": "FALSE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "legend_font_size_for_histogram", + "displayName": "Legend Font Size for Histogram", + "description": "Legend font size for the histogram.", + "paramType": "NUMBER", + "paramGroup": "Histogram", + "paramValues": null, + "defaultValue": "10", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "legend_position_for_histogram", + "displayName": "Legend Position for Histogram", + "description": "Legend position on histogram plot, can be 'none' if large number of samples", + "paramType": "SELECT", + "paramGroup": "Histogram", + "paramValues": [ + "top", + "bottom", + "left", + "right", + "none" + ], + "defaultValue": "top", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "number_of_histogram_legend_columns", + "displayName": "Number of Histogram Legend Columns", + "description": "", + "paramType": "NUMBER", + "paramGroup": "Histogram", + "paramValues": null, + "defaultValue": "6", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "colors_for_plots", + "displayName": "Colors for Plots", + "description": "Colors for the PCA and histogram will be picked, in order, from this list. If more colors are needed, program will choose from a wide range of random colors", + "paramType": "MULTISELECT", + "paramGroup": "Visualization", + "paramValues": [ + "#5954d6", + "#e1562c", + "#b80058", + "#00c6f8", + "#d163e6", + "#00a76c", + "#ff9287", + "#008cf9", + "#006e00", + "#796880", + "#FFA500", + "#878500" + ], + "defaultValue": null, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "interactive_plots", + "displayName": "Make Plots Interactive", + "description": "Toggle TRUE to make PCA and Histogram plots interactive, allowing you to hover your mouse over a point or line to view sample information. The similarity heatmap will not display if this toggle is set to TRUE. Default is FALSE.", + "paramType": "BOOLEAN", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": "FALSE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "plot_corr_matrix_heatmap", + "displayName": "Plot Correlation Matrix Heatmap", + "description": "Datasets with a large number of samples may be too large to create a correlation matix Heatmap. If Template takes longer than 5 min to run Toggle switch to off and the correlation matrix will not be be created", + "paramType": "BOOLEAN", + "paramGroup": "TCGA", + "paramValues": null, + "defaultValue": "TRUE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "save_plots", + "displayName": "Save Plots", + "description": "If this is `TRUE`, any plots generated during the analysis will be saved to disk.", + "paramType": "BOOLEAN", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "outputDatasetName": "Normalized Counts in MultiOmics Dataset", + "outputs": { + "multiOmicDataSet": { + "type": "file", + "name": "moo.rds" + }, + "figures": { + "type": "directory", + "name": "figures/norm/" + } + } +} \ No newline at end of file diff --git a/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/plot_expr_heatmap.json b/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/plot_expr_heatmap.json new file mode 100644 index 0000000..550d562 --- /dev/null +++ b/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/plot_expr_heatmap.json @@ -0,0 +1,567 @@ +{ + "title": "Plot Expression Heatmap", + "description": "This template is intended for use with Bulk RNA-seq data. It generates a heatmap for normalized (or batch corrected) RNA-seq data.\n\nThis template takes as input an expression matrix and your sample metadata table. The expression matrix is usually (though not always) going to consist of your normalized or batch corrected counts. It should always have one row per gene, a first column of gene names, and one additional column per sample.\n\nBy default, the samples (i.e. the columns) are allowed to cluster in an unsupervised fashion based on how similar their expression profiles are across the included genes. This can help identify samples that are non clustering with their group as you might expect based on the experimental design.\n\nAgain, by default, the top 500 genes by variance are used, as these are generally going to include those genes that most distinguish your samples from one another. You can change this as well as many other parameters about this heatmap if you explore the advanced options.", + "r_function": "plot_expr_heatmap", + "columns": [ + { + "key": "feature_id_colname", + "displayName": "Gene Column Name", + "description": "Column containing gene names.", + "paramGroup": "Data Setup", + "sourceDataset": "Counts_Matrix", + "defaultValue": null, + "columnType": "STRING", + "isMulti": null + }, + { + "key": "sample_id_colname", + "displayName": "Sample Name Column", + "description": "Column containing sample names.", + "paramGroup": "Data Setup", + "sourceDataset": "Sample_Metadata", + "defaultValue": null, + "columnType": "ALL", + "isMulti": null + }, + { + "key": "label_colname", + "displayName": "Sample Labels Column", + "description": "Select column from metadata that contains the sample names that will appear as column names on the heatmap.", + "paramGroup": "Data Setup", + "sourceDataset": "Sample_Metadata", + "defaultValue": null, + "columnType": "ALL", + "isMulti": null + }, + { + "key": "samples_to_include", + "displayName": "Samples to Include", + "description": "Select the sample columns from the input counts matrix that you want to include in the heatmap. Only numeric columns can be selected.", + "paramGroup": "Data Setup", + "sourceDataset": "Counts_Matrix", + "defaultValue": null, + "columnType": "NUMBER", + "isMulti": true + }, + { + "key": "reorder_dendrogram_order", + "displayName": "Reorder Sample Dendrogram Order", + "description": "Reorder the samples (columns) of the dendrogram by name, e.g. \u201csample2\u201d,\u201csample3\",\u201csample1\".", + "paramGroup": "Sample", + "sourceDataset": "Counts_Matrix", + "defaultValue": null, + "columnType": "ALL", + "isMulti": true + }, + { + "key": "group_colname", + "displayName": "Group Columns", + "description": "Columns containing the sample groups for annotation tracks", + "paramGroup": "Annotation", + "sourceDataset": "Sample_Metadata", + "defaultValue": null, + "columnType": "ALL", + "isMulti": true + } + ], + "inputDatasets": [ + { + "key": "moo_input_rds", + "displayName": "MOO input Rds", + "description": "File path to read the input multiOmicDataSet object (MOO)", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "parameters": [ + { + "key": "count_type", + "displayName": "Count Type", + "description": "", + "paramType": "STRING", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": "raw", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "sub_count_type", + "displayName": "Sub Count Type", + "description": "optional", + "paramType": "STRING", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": "raw", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "include_all_genes", + "displayName": "Include All Genes", + "description": "Set to TRUE if all genes are to be included. Set to FALSE if you want to filter genes by variance and/or provide a list of specific genes that will appear in the heatmap.", + "paramType": "BOOLEAN", + "paramGroup": "Gene", + "paramValues": null, + "defaultValue": "FALSE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "filter_top_genes_by_variance", + "displayName": "Filter Top Genes by Variance", + "description": "Set to TRUE if you want to only include the top genes by variance. Set to FALSE if you do not want to filter genes by variance.", + "paramType": "BOOLEAN", + "paramGroup": "Gene", + "paramValues": null, + "defaultValue": "TRUE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "top_genes_by_variance_to_include", + "displayName": "Top Genes by Variance to Include", + "description": "The number of genes to include if filtering genes by variance. This parameter is ignored if \"Filter top genes by variance\" is set to FALSE.", + "paramType": "NUMBER", + "paramGroup": "Gene", + "paramValues": null, + "defaultValue": "500", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "specific_genes_to_include_in_heatmap", + "displayName": "Specific Genes to Include in Heatmap", + "description": "Enter the gene symbols to be included in the heatmap, with each gene symbol separated with a space from the others. Alternatively, paste in a column of gene names from any spreadsheet application. This parameter is ignored if \"Include all genes\" is set to TRUE.", + "paramType": "STRING", + "paramGroup": "Gene", + "paramValues": null, + "defaultValue": "None", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "cluster_genes", + "displayName": "Cluster Genes", + "description": "Choose whether to cluster the rows (genes). If TRUE, rows will have clustering applied. If FALSE, clustering will not be applied to rows.", + "paramType": "BOOLEAN", + "paramGroup": "Gene", + "paramValues": null, + "defaultValue": "TRUE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "gene_clustering_method", + "displayName": "Gene Clustering Method", + "description": "Clustering method metric to be used in clustering samples.", + "paramType": "SELECT", + "paramGroup": "Gene", + "paramValues": [ + "ward.D", + "ward.D2", + "single", + "complete", + "average", + "mcquitty", + "median", + "centroid" + ], + "defaultValue": "average", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "gene_distance_metric", + "displayName": "Gene Distance Metric", + "description": "Distance metric to be used in clustering genes.", + "paramType": "SELECT", + "paramGroup": "Gene", + "paramValues": [ + "euclidean", + "maximum", + "manhattan", + "canberra", + "binary", + "minkowski", + "correlation" + ], + "defaultValue": "correlation", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "display_gene_dendrograms", + "displayName": "Display Gene Dendrogram", + "description": "Set to TRUE to show gene dendrograms. Set to FALSE to hide dendrograms.", + "paramType": "BOOLEAN", + "paramGroup": "Gene", + "paramValues": null, + "defaultValue": "TRUE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "display_gene_names", + "displayName": "Display Gene Names", + "description": "Set to TRUE to display gene names on the right side of the heatmap. Set to FALSE to hide gene names.", + "paramType": "BOOLEAN", + "paramGroup": "Gene", + "paramValues": null, + "defaultValue": "FALSE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "center_and_rescale_expression", + "displayName": "Center and Rescale Expression", + "description": "Center and rescale expression for each gene across all included samples.", + "paramType": "BOOLEAN", + "paramGroup": "Gene", + "paramValues": null, + "defaultValue": "TRUE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "cluster_samples", + "displayName": "Cluster Samples", + "description": "Choose whether to cluster the columns (samples). If TRUE, columns will have clustering applied. If FALSE, clustering will not be applied to columns.", + "paramType": "BOOLEAN", + "paramGroup": "Sample", + "paramValues": null, + "defaultValue": "TRUE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "arrange_sample_columns", + "displayName": "Arrange Sample Columns", + "description": "If TRUE, your samples will be arranged by the order that Groups are found in the \"Samples to Include\" parameter above. If FALSE, and \"Cluster Samples\" is FALSE, and \"Order by Gene Expression is FALSE, then samples will appear in the order of input (Samples to Include).", + "paramType": "BOOLEAN", + "paramGroup": "Sample", + "paramValues": null, + "defaultValue": "FALSE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "order_by_gene_expression", + "displayName": "Order by Gene Expression", + "description": "If TRUE, set gene name below and direction for ordering", + "paramType": "BOOLEAN", + "paramGroup": "Sample", + "paramValues": null, + "defaultValue": "FALSE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "gene_to_order_columns", + "displayName": "Gene to Order Columns", + "description": "Gene to order columns by expression levels", + "paramType": "STRING", + "paramGroup": "Sample", + "paramValues": null, + "defaultValue": " ", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "gene_expression_order", + "displayName": "Gene Expression Order", + "description": "Choose direction for gene order", + "paramType": "SELECT", + "paramGroup": "Sample", + "paramValues": [ + "low_to_high", + "high_to_low" + ], + "defaultValue": "low_to_high", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "smpl_clustering_method", + "displayName": "Sample Clustering Method", + "description": "Clustering method to be used in clustering samples.", + "paramType": "SELECT", + "paramGroup": "Sample", + "paramValues": [ + "ward.D", + "ward.D2", + "single", + "complete", + "average", + "mcquitty", + "median", + "centroid" + ], + "defaultValue": " ", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "smpl_distance_metric", + "displayName": "Sample Distance Metric", + "description": "Distance metric to be used in clustering samples.", + "paramType": "SELECT", + "paramGroup": "Sample", + "paramValues": [ + "euclidean", + "maximum", + "manhattan", + "canberra", + "binary", + "minkowski", + "correlation" + ], + "defaultValue": "correlation", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "display_smpl_dendrograms", + "displayName": "Display Sample Dendrograms", + "description": "Set to TRUE to show sample dendrograms. Set to FALSE to hide dendrogram.", + "paramType": "BOOLEAN", + "paramGroup": "Sample", + "paramValues": null, + "defaultValue": "TRUE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "reorder_dendrogram", + "displayName": "Reorder Sample Dendrogram", + "description": "If TRUE, set the order of the dendrogram (below)", + "paramType": "BOOLEAN", + "paramGroup": "Sample", + "paramValues": null, + "defaultValue": "FALSE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "display_sample_names", + "displayName": "Display Sample Names", + "description": "Set to TRUE if you want sample names to be displayed on the plot. Set to FALSE to hide sample names.", + "paramType": "BOOLEAN", + "paramGroup": "Sample", + "paramValues": null, + "defaultValue": "TRUE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "assign_group_colors", + "displayName": "Assign Group Colors", + "description": "If TRUE, set the groups assigned colors (below)", + "paramType": "BOOLEAN", + "paramGroup": "Annotation", + "paramValues": null, + "defaultValue": "FALSE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "assign_color_to_sample_groups", + "displayName": "Assign Color to Sample Groups", + "description": "Enter each sample to color in the format: group_name: color This parameter is ignored if \"Assign Colors\" is set to FALSE. Use this link to select colors: https://nidap.nih.gov/workspace/preview-app/ri.blobster.main.pdf.7922ce2b-39d7-40e7-85ea-8b8146bbf363", + "paramType": "VECTOR", + "paramGroup": "Annotation", + "paramValues": null, + "defaultValue": "c()", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "group_colors", + "displayName": "Group Colors", + "description": "Set group annotation colors.", + "paramType": "MULTISELECT", + "paramGroup": "Annotation", + "paramValues": [ + "#5954d6", + "#e1562c", + "#b80058", + "#00c6f8", + "#d163e6", + "#00a76c", + "#ff9287", + "#008cf9", + "#006e00", + "#796880", + "#FFA500", + "#878500" + ], + "defaultValue": null, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "heatmap_color_scheme", + "displayName": "Heatmap Color Scheme", + "description": "Color scheme for heatmap.", + "paramType": "SELECT", + "paramGroup": "Visual", + "paramValues": [ + "Default", + "Blue to Red", + "Red to Vanilla", + "Violet to Pink", + "Bu Yl Rd", + "Bu Wt Rd" + ], + "defaultValue": "Default", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "autoscale_heatmap_color", + "displayName": "Autoscale Heatmap Color", + "description": "Set to TRUE to autoscale the heatmap colors between the maximum and minimum heatmap color parameters. If FALSE, set the heatmap colors between \"Set max heatmap color\" and \"Set min heatmap color\" (below).", + "paramType": "BOOLEAN", + "paramGroup": "Visual", + "paramValues": null, + "defaultValue": "TRUE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "set_max_heatmap_color", + "displayName": "Set Max Heatmap Color", + "description": "If Autoscale heatmap color is set to FALSE, set the maximum heatmap z-score value.", + "paramType": "NUMBER", + "paramGroup": "Visual", + "paramValues": null, + "defaultValue": "2", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "set_min_heatmap_color", + "displayName": "Set Min Heatmap Color", + "description": "If Autoscale heatmap color is set to FALSE, set the minimum heatmap z-score value.", + "paramType": "NUMBER", + "paramGroup": "Visual", + "paramValues": null, + "defaultValue": "-2", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "aspect_ratio", + "displayName": "Aspect Ratio", + "description": "Set figure Aspect Ratio. Ratio refers to entire figure including legend. If set to Auto figure size is based on number of rows and columns form counts matrix. default - Auto", + "paramType": "STRING", + "paramGroup": "Visual", + "paramValues": null, + "defaultValue": "Auto", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "display_numbers", + "displayName": "Display Numbers", + "description": "Setting to FALSE (default) will not display numerical value of heat on heatmap. Set to TRUE if you want to see these numbers on the plot.", + "paramType": "BOOLEAN", + "paramGroup": "Visual", + "paramValues": null, + "defaultValue": "FALSE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "gene_name_font_size", + "displayName": "Gene Name Font Size", + "description": "Font size for gene names. If you don't want gene labels to show, toggle \"Display Gene Names\" below to FALSE", + "paramType": "NUMBER", + "paramGroup": "Visual", + "paramValues": null, + "defaultValue": "4", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "legend_font_size", + "displayName": "Legend Font Size", + "description": "Set Font size for figure legend. Default is 10.", + "paramType": "NUMBER", + "paramGroup": "Visual", + "paramValues": null, + "defaultValue": "10", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "sample_name_font_size", + "displayName": "Sample Name Font Size", + "description": "Font size for sample names. If you don't want to display samples names, toggle \"Display sample names\" (below) to FALSE", + "paramType": "NUMBER", + "paramGroup": "Visual", + "paramValues": null, + "defaultValue": "8", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "save_plots", + "displayName": "Save Plots", + "description": "If this is `TRUE`, any plots generated during the analysis will be saved to disk.", + "paramType": "BOOLEAN", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "outputDatasetName": "Expression Heatmap Plot", + "outputs": { + "figures": { + "type": "file", + "name": "figures/heatmap/expr_heatmap.png" + } + } +} \ No newline at end of file diff --git a/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/plot_pca_2d.json b/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/plot_pca_2d.json new file mode 100644 index 0000000..8565011 --- /dev/null +++ b/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/plot_pca_2d.json @@ -0,0 +1,296 @@ +{ + "title": "PCA 2D", + "description": "This template is based on Bulk RNA-seq QC PCA template and is intended to provide a 2D PCA plot generated from the data.", + "r_function": "plot_pca_2d", + "columns": [ + { + "key": "feature_id_colname", + "displayName": "FeatureID Name Column", + "description": "The column from your counts matrix containing the Feature IDs (such as gene names, isoform names and so on). This is usually the first column of your counts matrix.", + "paramGroup": "Basic", + "sourceDataset": "Counts_Matrix", + "defaultValue": null, + "columnType": "STRING", + "isMulti": null + }, + { + "key": "sample_id_colname", + "displayName": "Sample Names Column", + "description": "The column from your sample metadata table containing the sample names. These should be the same as the sample names found in the column names of the counts matrix.", + "paramGroup": "Basic", + "sourceDataset": "Sample_Metadata_Table", + "defaultValue": null, + "columnType": "STRING", + "isMulti": null + }, + { + "key": "group_colname", + "displayName": "Group Column", + "description": "The column from your sample metadata table containing sample group information. This is usually a column showing which of your experimental treatments each sample belongs to (e.g. WildType, Knockout, Tumor, Normal, Before, After, etc.).", + "paramGroup": "Basic", + "sourceDataset": "Sample_Metadata_Table", + "defaultValue": "Group", + "columnType": "ALL", + "isMulti": null + }, + { + "key": "label_colname", + "displayName": "Plot Labels Column", + "description": "The column from your sample metadata table containing the sample names as you wish them to appear in the QC figure. This is often the same Sample Name Column (see parameter above). However, you may desire different labels to display on your PCA figure (e.g. shorter labels). These labels can be added as an additional column in your metadata table and used here to label your plot.", + "paramGroup": "Basic", + "sourceDataset": "Sample_Metadata_Table", + "defaultValue": "Label", + "columnType": "ALL", + "isMulti": null + } + ], + "inputDatasets": [ + { + "key": "moo_input_rds", + "displayName": "MOO input Rds", + "description": "File path to read the input multiOmicDataSet object (MOO)", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "parameters": [ + { + "key": "count_type", + "displayName": "Count Type", + "description": "The type of counts to use from the multiOmicDataSet counts slot", + "paramType": "STRING", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": "raw", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "sub_count_type", + "displayName": "Sub Count Type", + "description": "Used if count_type is a list in the counts slot: specify the sub count type within the list (optional)", + "paramType": "STRING", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": "raw", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "principal_components", + "displayName": "Principal Components", + "description": "Vector with numbered principal components to plot. For 2D PCA, specify exactly 2 components (e.g., [1, 2] for PC1 vs PC2).", + "paramType": "MULTISELECT", + "paramGroup": "Basic", + "paramValues": [ + 1, + 2, + 3, + 4, + 5 + ], + "defaultValue": [ + 1, + 2 + ], + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "point_size", + "displayName": "Point Size", + "description": "The size of the points in the 2D PCA plot.", + "paramType": "NUMBER", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": 1, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "add_label", + "displayName": "Add Labels", + "description": "Whether to add text labels for the points on the plot.", + "paramType": "BOOLEAN", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "label_font_size", + "displayName": "Label Font Size", + "description": "The font size for point labels (if add_label is TRUE).", + "paramType": "NUMBER", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": 3, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "legend_position", + "displayName": "Legend Position", + "description": "Position of the legend on the plot.", + "paramType": "SELECT", + "paramGroup": "Visualization", + "paramValues": [ + "top", + "bottom", + "left", + "right", + "none" + ], + "defaultValue": "top", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "color_values", + "displayName": "Color Values", + "description": "Colors for the PCA will be picked, in order, from this list. There are thousands of colors. You may remove or add colors as you choose, but take care that there are always at least as many colors in this list than you need to color items in your plot.\n\nExample: if you are coloring by Group and have 3 groups, you should have at least 3 colors in your list.", + "paramType": "MULTISELECT", + "paramGroup": "Visualization", + "paramValues": [ + "slateblue3", + "tomato2", + "maroon", + "deepskyblue", + "mediumorchid2", + "mediumseagreen", + "salmon", + "dodgerblue", + "darkgreen", + "plum4", + "orange", + "yellow4", + "aquamarine3", + "salmon1", + "lightskyblue3", + "plum3", + "firebrick", + "darkolivegreen3", + "goldenrod1", + "burlywood2", + "gray70", + "firebrick2", + "steelblue", + "palegreen4", + "orchid4", + "darkorange1", + "yellow", + "sienna", + "palevioletred1", + "gray60", + "cyan4", + "darkorange3", + "mediumpurple3", + "violetred2", + "olivedrab", + "darkgoldenrod2", + "darkgoldenrod", + "gray40", + "palegreen3", + "thistle3", + "khaki1", + "deeppink2", + "chocolate3", + "paleturquoise3", + "wheat1", + "lightsteelblue", + "sandybrown", + "darkolivegreen2", + "thistle2", + "gray85", + "orchid3", + "darkseagreen1", + "lightgoldenrod1", + "lightskyblue2", + "dodgerblue3", + "darkseagreen3", + "forestgreen", + "lightpink2", + "mediumpurple4", + "lightpink1", + "thistle", + "navajowhite", + "lemonchiffon", + "bisque2", + "mistyrose", + "gray95", + "lightcyan3", + "peachpuff2", + "lightsteelblue2", + "lightyellow2", + "moccasin", + "antiquewhite2", + "gray80", + "lightgrey" + ], + "defaultValue": [ + "#5954d6", + "#e1562c", + "#b80058", + "#00c6f8", + "#d163e6", + "#00a76c", + "#ff9287", + "#008cf9", + "#006e00", + "#796880", + "#FFA500", + "#878500" + ], + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "interactive_plots", + "displayName": "Interactive Plots", + "description": "If TRUE, creates an interactive plotly plot instead of a static ggplot.", + "paramType": "BOOLEAN", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": false, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "save_plots", + "displayName": "Save Plots", + "description": "If this is `TRUE`, any plots generated during the analysis will be saved to disk.", + "paramType": "BOOLEAN", + "paramGroup": "Visualization", + "paramValues": [ + true, + false + ], + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "outputDatasetName": "2D PCA Plot", + "outputs": { + "figures": { + "type": "file", + "name": "figures/pca/pca_2D.png" + } + } +} \ No newline at end of file diff --git a/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/plot_pca_3d.json b/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/plot_pca_3d.json new file mode 100644 index 0000000..39b95b4 --- /dev/null +++ b/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/plot_pca_3d.json @@ -0,0 +1,217 @@ +{ + "title": "PCA 3D", + "description": "This template is based on Bulk RNA-seq QC PCA template and is intended to provide interactive 3D view of a PCA plot generated from the data.", + "r_function": "plot_pca_3d", + "columns": [ + { + "key": "feature_id_colname", + "displayName": "FeatureID Name Column", + "description": "The column from your counts matrix containing the Feature IDs (such as gene names, isoform names and so on). This is usually the first column of your counts matrix.", + "paramGroup": "Basic", + "sourceDataset": "Counts_Matrix", + "defaultValue": null, + "columnType": "STRING", + "isMulti": null + }, + { + "key": "sample_id_colname", + "displayName": "Sample Names Column", + "description": "The column from your sample metadata table containing the sample names. These should be the same as the sample names found in the column names of the counts matrix.", + "paramGroup": "Basic", + "sourceDataset": "Sample_Metadata_Table", + "defaultValue": null, + "columnType": "STRING", + "isMulti": null + }, + { + "key": "group_colname", + "displayName": "Group Column", + "description": "The column from your sample metadata table containing sample group information. This is usually a column showing which of your experimental treatments each sample belongs to (e.g. WildType, Knockout, Tumor, Normal, Before, After, etc.).", + "paramGroup": "Basic", + "sourceDataset": "Sample_Metadata_Table", + "defaultValue": null, + "columnType": "ALL", + "isMulti": null + }, + { + "key": "label_colname", + "displayName": "Plot Labels Column", + "description": "The column from your sample metadata table containing the sample names as you wish them to appear in the QC figure. This is often the same Sample Name Column (see parameter above). However, you may desire different labels to display on your PCA figure (e.g. shorter labels). These labels can be added as an additional column in your metadata table and used here to label your plot.", + "paramGroup": "Basic", + "sourceDataset": "Sample_Metadata_Table", + "defaultValue": null, + "columnType": "ALL", + "isMulti": null + } + ], + "inputDatasets": [ + { + "key": "moo_input_rds", + "displayName": "MOO input Rds", + "description": "File path to read the input multiOmicDataSet object (MOO)", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "parameters": [ + { + "key": "count_type", + "displayName": "Count Type", + "description": "", + "paramType": "STRING", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": "raw", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "sub_count_type", + "displayName": "Sub Count Type", + "description": "optional", + "paramType": "STRING", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": "raw", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "point_size", + "displayName": "Point Size", + "description": "The size of the points in the 3D PCA plot.", + "paramType": "NUMBER", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": "8", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "color_values", + "displayName": "Color Values", + "description": "Colors for the PCA will be picked, in order, from this list. There are thousands of colors. You may remove or add colors as you choose, but take care that there are always at least as many colors in this list than you need to color items in your plot.\n\nExample: if you are coloring by Group and have 3 groups, you should have at least 3 colors in your list.", + "paramType": "MULTISELECT", + "paramGroup": "Visualization", + "paramValues": [ + "slateblue3", + "tomato2", + "maroon", + "deepskyblue", + "mediumorchid2", + "mediumseagreen", + "salmon", + "dodgerblue", + "darkgreen", + "plum4", + "orange", + "yellow4", + "aquamarine3", + "salmon1", + "lightskyblue3", + "plum3", + "firebrick", + "darkolivegreen3", + "goldenrod1", + "burlywood2", + "gray70", + "firebrick2", + "steelblue", + "palegreen4", + "orchid4", + "darkorange1", + "yellow", + "sienna", + "palevioletred1", + "gray60", + "cyan4", + "darkorange3", + "mediumpurple3", + "violetred2", + "olivedrab", + "darkgoldenrod2", + "darkgoldenrod", + "gray40", + "palegreen3", + "thistle3", + "khaki1", + "deeppink2", + "chocolate3", + "paleturquoise3", + "wheat1", + "lightsteelblue", + "sandybrown", + "darkolivegreen2", + "thistle2", + "gray85", + "orchid3", + "darkseagreen1", + "lightgoldenrod1", + "lightskyblue2", + "dodgerblue3", + "darkseagreen3", + "forestgreen", + "lightpink2", + "mediumpurple4", + "lightpink1", + "thistle", + "navajowhite", + "lemonchiffon", + "bisque2", + "mistyrose", + "gray95", + "lightcyan3", + "peachpuff2", + "lightsteelblue2", + "lightyellow2", + "moccasin", + "antiquewhite2", + "gray80", + "lightgrey" + ], + "defaultValue": "c(\"slateblue3\",\"tomato2\",\"maroon\",\"deepskyblue\",\"mediumorchid2\",\"mediumseagreen\",\"salmon\",\"dodgerblue\",\"darkgreen\",\"plum4\",\"orange\",\"yellow4\")", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "plot_title", + "displayName": "Plot Title", + "description": "", + "paramType": "STRING", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": "PCA 3D", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "save_plots", + "displayName": "Save Plots", + "description": "If this is `TRUE`, any plots generated during the analysis will be saved to disk.", + "paramType": "BOOLEAN", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "outputDatasetName": "3D PCA Plot", + "outputs": { + "figures": { + "type": "file", + "name": "figures/pca/pca_3D.html" + } + } +} \ No newline at end of file diff --git a/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/plot_venn_diagram.json b/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/plot_venn_diagram.json new file mode 100644 index 0000000..c163c04 --- /dev/null +++ b/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/plot_venn_diagram.json @@ -0,0 +1,1106 @@ +{ + "title": "Venn Diagram", + "description": "Template generates Venn diagram of intersections across a series of sets (e.g., intersections of significant genes across tested contrasts).\nThis Venn diagram is available for up to five sets; Intersection plot is available for any number of sets. Specific sets can be selected for the visualizations and the returned dataset may include all (default) or specified intersections.\n", + "r_function": "plot_venn_diagram", + "columns": [ + { + "key": "feature_id_colname", + "displayName": "Elements Column", + "description": "Column containing the names of elements. These elements will be counted and the number displayed in each intersection of your Venn diagram. Commonly this will be the Genes column of the output of the \"Volcno Plot. -Summary\" template.", + "paramGroup": "Basic", + "sourceDataset": "Input_Dataset", + "defaultValue": null, + "columnType": "STRING", + "isMulti": null + }, + { + "key": "contrasts_colname", + "displayName": "Categories Column", + "description": "Column containing the category names. These categories will be used to draw the circles of your Venn diagram. Commonly, this will be your Contrasts column from the output of the \"Volcano Plot - Summary\" template.", + "paramGroup": "Basic", + "sourceDataset": "Input_Dataset", + "defaultValue": null, + "columnType": "STRING", + "isMulti": null + } + ], + "inputDatasets": [ + { + "key": "moo_input_rds", + "displayName": "DataFrame input Rds", + "description": "File path to read the summary dataframe (e.g. from plot_volcano_summary output)", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "summary_dataframe.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "parameters": [ + { + "key": "moo_output_rds", + "displayName": "Venn diagram DataFrame Rds", + "description": "File path to output the venn diagram DataFrame as an Rds file", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "select_contrasts", + "displayName": "Selected Categories", + "description": "If no categories are listed then all available categories will be used; if a single category is listed only Venn diagram or Intersection table can be plotted; if more than 5 categories are listed only Intersection plot or Intersection table can be plotted", + "paramType": "VECTOR", + "paramGroup": "Advanced", + "paramValues": null, + "defaultValue": "c()", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "plot_type", + "displayName": "Select Plot Type", + "description": "", + "paramType": "SELECT", + "paramGroup": "Advanced", + "paramValues": [ + "Venn diagram", + "Intersection plot", + "Intersection table" + ], + "defaultValue": "Venn diagram", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "intersection_ids", + "displayName": "Intersection IDs", + "description": "Enter Intersection id(s); the intersection id displayed in the Logs tab after the first run of the template or in the Intersection table if selected as the option of the Plot selection parameter above; if none entered, all intersections are returned", + "paramType": "VECTOR", + "paramGroup": "Advanced", + "paramValues": null, + "defaultValue": "c()", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "venn_force_unique", + "displayName": "Venn Force Unique", + "description": "If TRUE, count each element in a given category only once (ignore duplicate entries)", + "paramType": "BOOLEAN", + "paramGroup": "Venn Diagram", + "paramValues": null, + "defaultValue": "TRUE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "venn_numbers_format", + "displayName": "Venn Numbers Format", + "description": "The format that the numbers will be printed in", + "paramType": "SELECT", + "paramGroup": "Venn Diagram", + "paramValues": [ + "raw", + "percent", + "raw-percent", + "percent-raw" + ], + "defaultValue": "raw", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "venn_significant_digits", + "displayName": "Venn Significant Digits", + "description": "The number of significant digits in percent values", + "paramType": "NUMBER", + "paramGroup": "Venn Diagram", + "paramValues": null, + "defaultValue": "2", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "venn_fill_colors", + "displayName": "Venn Fill Colors", + "description": "The colour of each circle's interior. The number of colors you choose should be at least the number of input datasets.", + "paramType": "MULTISELECT", + "paramGroup": "Venn Diagram", + "paramValues": [ + "white", + "aliceblue", + "antiquewhite", + "antiquewhite1", + "antiquewhite2", + "antiquewhite3", + "antiquewhite4", + "aquamarine", + "aquamarine1", + "aquamarine2", + "aquamarine3", + "aquamarine4", + "azure", + "azure1", + "azure2", + "azure3", + "azure4", + "beige", + "bisque", + "bisque1", + "bisque2", + "bisque3", + "bisque4", + "black", + "blanchedalmond", + "blue", + "blue1", + "blue2", + "blue3", + "blue4", + "blueviolet", + "brown", + "brown1", + "brown2", + "brown3", + "brown4", + "burlywood", + "burlywood1", + "burlywood2", + "burlywood3", + "burlywood4", + "cadetblue", + "cadetblue1", + "cadetblue2", + "cadetblue3", + "cadetblue4", + "chartreuse", + "chartreuse1", + "chartreuse2", + "chartreuse3", + "chartreuse4", + "chocolate", + "chocolate1", + "chocolate2", + "chocolate3", + "chocolate4", + "coral", + "coral1", + "coral2", + "coral3", + "coral4", + "cornflowerblue", + "cornsilk", + "cornsilk1", + "cornsilk2", + "cornsilk3", + "cornsilk4", + "cyan", + "cyan1", + "cyan2", + "cyan3", + "cyan4", + "darkblue", + "darkcyan", + "darkgoldenrod", + "darkgoldenrod1", + "darkgoldenrod2", + "darkgoldenrod3", + "darkgoldenrod4", + "darkgray", + "darkgreen", + "darkgrey", + "darkkhaki", + "darkmagenta", + "darkolivegreen", + "darkolivegreen1", + "darkolivegreen2", + "darkolivegreen3", + "darkolivegreen4", + "darkorange", + "darkorange1", + "darkorange2", + "darkorange3", + "darkorange4", + "darkorchid", + "darkorchid1", + "darkorchid2", + "darkorchid3", + "darkorchid4", + "darkred", + "darksalmon", + "darkseagreen", + "darkseagreen1", + "darkseagreen2", + "darkseagreen3", + "darkseagreen4", + "darkslateblue", + "darkslategray", + "darkslategray1", + "darkslategray2", + "darkslategray3", + "darkslategray4", + "darkslategrey", + "darkturquoise", + "darkviolet", + "deeppink", + "deeppink1", + "deeppink2", + "deeppink3", + "deeppink4", + "deepskyblue", + "deepskyblue1", + "deepskyblue2", + "deepskyblue3", + "deepskyblue4", + "dimgray", + "dimgrey", + "dodgerblue", + "dodgerblue1", + "dodgerblue2", + "dodgerblue3", + "dodgerblue4", + "firebrick", + "firebrick1", + "firebrick2", + "firebrick3", + "firebrick4", + "floralwhite", + "forestgreen", + "gainsboro", + "ghostwhite", + "gold", + "gold1", + "gold2", + "gold3", + "gold4", + "goldenrod", + "goldenrod1", + "goldenrod2", + "goldenrod3", + "goldenrod4", + "gray", + "gray0", + "gray1", + "gray2", + "gray3", + "gray4", + "gray5", + "gray6", + "gray7", + "gray8", + "gray9", + "gray10", + "gray11", + "gray12", + "gray13", + "gray14", + "gray15", + "gray16", + "gray17", + "gray18", + "gray19", + "gray20", + "gray21", + "gray22", + "gray23", + "gray24", + "gray25", + "gray26", + "gray27", + "gray28", + "gray29", + "gray30", + "gray31", + "gray32", + "gray33", + "gray34", + "gray35", + "gray36", + "gray37", + "gray38", + "gray39", + "gray40", + "gray41", + "gray42", + "gray43", + "gray44", + "gray45", + "gray46", + "gray47", + "gray48", + "gray49", + "gray50", + "gray51", + "gray52", + "gray53", + "gray54", + "gray55", + "gray56", + "gray57", + "gray58", + "gray59", + "gray60", + "gray61", + "gray62", + "gray63", + "gray64", + "gray65", + "gray66", + "gray67", + "gray68", + "gray69", + "gray70", + "gray71", + "gray72", + "gray73", + "gray74", + "gray75", + "gray76", + "gray77", + "gray78", + "gray79", + "gray80", + "gray81", + "gray82", + "gray83", + "gray84", + "gray85", + "gray86", + "gray87", + "gray88", + "gray89", + "gray90", + "gray91", + "gray92", + "gray93", + "gray94", + "gray95", + "gray96", + "gray97", + "gray98", + "gray99", + "gray100", + "green", + "green1", + "green2", + "green3", + "green4", + "greenyellow", + "grey", + "grey0", + "grey1", + "grey2", + "grey3", + "grey4", + "grey5", + "grey6", + "grey7", + "grey8", + "grey9", + "grey10", + "grey11", + "grey12", + "grey13", + "grey14", + "grey15", + "grey16", + "grey17", + "grey18", + "grey19", + "grey20", + "grey21", + "grey22", + "grey23", + "grey24", + "grey25", + "grey26", + "grey27", + "grey28", + "grey29", + "grey30", + "grey31", + "grey32", + "grey33", + "grey34", + "grey35", + "grey36", + "grey37", + "grey38", + "grey39", + "grey40", + "grey41", + "grey42", + "grey43", + "grey44", + "grey45", + "grey46", + "grey47", + "grey48", + "grey49", + "grey50", + "grey51", + "grey52", + "grey53", + "grey54", + "grey55", + "grey56", + "grey57", + "grey58", + "grey59", + "grey60", + "grey61", + "grey62", + "grey63", + "grey64", + "grey65", + "grey66", + "grey67", + "grey68", + "grey69", + "grey70", + "grey71", + "grey72", + "grey73", + "grey74", + "grey75", + "grey76", + "grey77", + "grey78", + "grey79", + "grey80", + "grey81", + "grey82", + "grey83", + "grey84", + "grey85", + "grey86", + "grey87", + "grey88", + "grey89", + "grey90", + "grey91", + "grey92", + "grey93", + "grey94", + "grey95", + "grey96", + "grey97", + "grey98", + "grey99", + "grey100", + "honeydew", + "honeydew1", + "honeydew2", + "honeydew3", + "honeydew4", + "hotpink", + "hotpink1", + "hotpink2", + "hotpink3", + "hotpink4", + "indianred", + "indianred1", + "indianred2", + "indianred3", + "indianred4", + "ivory", + "ivory1", + "ivory2", + "ivory3", + "ivory4", + "khaki", + "khaki1", + "khaki2", + "khaki3", + "khaki4", + "lavender", + "lavenderblush", + "lavenderblush1", + "lavenderblush2", + "lavenderblush3", + "lavenderblush4", + "lawngreen", + "lemonchiffon", + "lemonchiffon1", + "lemonchiffon2", + "lemonchiffon3", + "lemonchiffon4", + "lightblue", + "lightblue1", + "lightblue2", + "lightblue3", + "lightblue4", + "lightcoral", + "lightcyan", + "lightcyan1", + "lightcyan2", + "lightcyan3", + "lightcyan4", + "lightgoldenrod", + "lightgoldenrod1", + "lightgoldenrod2", + "lightgoldenrod3", + "lightgoldenrod4", + "lightgoldenrodyellow", + "lightgray", + "lightgreen", + "lightgrey", + "lightpink", + "lightpink1", + "lightpink2", + "lightpink3", + "lightpink4", + "lightsalmon", + "lightsalmon1", + "lightsalmon2", + "lightsalmon3", + "lightsalmon4", + "lightseagreen", + "lightskyblue", + "lightskyblue1", + "lightskyblue2", + "lightskyblue3", + "lightskyblue4", + "lightslateblue", + "lightslategray", + "lightslategrey", + "lightsteelblue", + "lightsteelblue1", + "lightsteelblue2", + "lightsteelblue3", + "lightsteelblue4", + "lightyellow", + "lightyellow1", + "lightyellow2", + "lightyellow3", + "lightyellow4", + "limegreen", + "linen", + "magenta", + "magenta1", + "magenta2", + "magenta3", + "magenta4", + "maroon", + "maroon1", + "maroon2", + "maroon3", + "maroon4", + "mediumaquamarine", + "mediumblue", + "mediumorchid", + "mediumorchid1", + "mediumorchid2", + "mediumorchid3", + "mediumorchid4", + "mediumpurple", + "mediumpurple1", + "mediumpurple2", + "mediumpurple3", + "mediumpurple4", + "mediumseagreen", + "mediumslateblue", + "mediumspringgreen", + "mediumturquoise", + "mediumvioletred", + "midnightblue", + "mintcream", + "mistyrose", + "mistyrose1", + "mistyrose2", + "mistyrose3", + "mistyrose4", + "moccasin", + "navajowhite", + "navajowhite1", + "navajowhite2", + "navajowhite3", + "navajowhite4", + "navy", + "navyblue", + "oldlace", + "olivedrab", + "olivedrab1", + "olivedrab2", + "olivedrab3", + "olivedrab4", + "orange", + "orange1", + "orange2", + "orange3", + "orange4", + "orangered", + "orangered1", + "orangered2", + "orangered3", + "orangered4", + "orchid", + "orchid1", + "orchid2", + "orchid3", + "orchid4", + "palegoldenrod", + "palegreen", + "palegreen1", + "palegreen2", + "palegreen3", + "palegreen4", + "paleturquoise", + "paleturquoise1", + "paleturquoise2", + "paleturquoise3", + "paleturquoise4", + "palevioletred", + "palevioletred1", + "palevioletred2", + "palevioletred3", + "palevioletred4", + "papayawhip", + "peachpuff", + "peachpuff1", + "peachpuff2", + "peachpuff3", + "peachpuff4", + "peru", + "pink", + "pink1", + "pink2", + "pink3", + "pink4", + "plum", + "plum1", + "plum2", + "plum3", + "plum4", + "powderblue", + "purple", + "purple1", + "purple2", + "purple3", + "purple4", + "red", + "red1", + "red2", + "red3", + "red4", + "rosybrown", + "rosybrown1", + "rosybrown2", + "rosybrown3", + "rosybrown4", + "royalblue", + "royalblue1", + "royalblue2", + "royalblue3", + "royalblue4", + "saddlebrown", + "salmon", + "salmon1", + "salmon2", + "salmon3", + "salmon4", + "sandybrown", + "seagreen", + "seagreen1", + "seagreen2", + "seagreen3", + "seagreen4", + "seashell", + "seashell1", + "seashell2", + "seashell3", + "seashell4", + "sienna", + "sienna1", + "sienna2", + "sienna3", + "sienna4", + "skyblue", + "skyblue1", + "skyblue2", + "skyblue3", + "skyblue4", + "slateblue", + "slateblue1", + "slateblue2", + "slateblue3", + "slateblue4", + "slategray", + "slategray1", + "slategray2", + "slategray3", + "slategray4", + "slategrey", + "snow", + "snow1", + "snow2", + "snow3", + "snow4", + "springgreen", + "springgreen1", + "springgreen2", + "springgreen3", + "springgreen4", + "steelblue", + "steelblue1", + "steelblue2", + "steelblue3", + "steelblue4", + "tan", + "tan1", + "tan2", + "tan3", + "tan4", + "thistle", + "thistle1", + "thistle2", + "thistle3", + "thistle4", + "tomato", + "tomato1", + "tomato2", + "tomato3", + "tomato4", + "turquoise", + "turquoise1", + "turquoise2", + "turquoise3", + "turquoise4", + "violet", + "violetred", + "violetred1", + "violetred2", + "violetred3", + "violetred4", + "wheat", + "wheat1", + "wheat2", + "wheat3", + "wheat4", + "whitesmoke", + "yellow", + "yellow1", + "yellow2", + "yellow3", + "yellow4", + "yellowgreen" + ], + "defaultValue": "c(\"darkgoldenrod2\",\"darkolivegreen2\",\"mediumpurple3\",\"darkorange2\",\"lightgreen\")", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "venn_fill_transparency", + "displayName": "Venn Fill Transparency", + "description": "The transparency of each circle's interior. Enter a value between 0 and 1 (from transparent to opaque)", + "paramType": "STRING", + "paramGroup": "Venn Diagram", + "paramValues": null, + "defaultValue": "0.2", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "venn_border_colors", + "displayName": "Venn Border Colors", + "description": "The colour of each circle's circumference; if the option 'fill colors' is chosen the same as \"Colors: fill\" above", + "paramType": "SELECT", + "paramGroup": "Venn Diagram", + "paramValues": [ + "black", + "fill colors" + ], + "defaultValue": "fill colors", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "venn_font_size_for_category_names", + "displayName": "Venn Font Size for Category Names", + "description": "The font size for each category name", + "paramType": "NUMBER", + "paramGroup": "Venn Diagram", + "paramValues": null, + "defaultValue": "3", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "venn_category_names_distance", + "displayName": "Venn Category Names Distance", + "description": "A numeric vector giving the distance of each category name from the edge of the circle (can be negative); the default values are between 0.025 - 0.22; adjusting both the distance and position (below) may be optimal.", + "paramType": "VECTOR", + "paramGroup": "Venn Diagram", + "paramValues": null, + "defaultValue": "c()", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "venn_category_names_position", + "displayName": "Venn Category Names Position", + "description": "A numeric vector giving the position (in degrees) of each category name along the circle, with 0 at 12 o'clock; adjusting both the position and distance (above) may be optimal.", + "paramType": "VECTOR", + "paramGroup": "Venn Diagram", + "paramValues": null, + "defaultValue": "c()", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "venn_font_size_for_counts", + "displayName": "Venn Font Size for Counts", + "description": "The font size for each area label", + "paramType": "NUMBER", + "paramGroup": "Venn Diagram", + "paramValues": null, + "defaultValue": "6", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "venn_outer_margin", + "displayName": "Venn Outer Margin", + "description": "The amount of whitespace around the diagram in grid units; recommended values are between 0.05 - 0.2; adding more space can help fit the category names.", + "paramType": "NUMBER", + "paramGroup": "Venn Diagram", + "paramValues": null, + "defaultValue": "0", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "intersections_order", + "displayName": "Intersections Order", + "description": "The intersections ordering; the options include degree and freq (frequency)", + "paramType": "SELECT", + "paramGroup": "Intersection Plot", + "paramValues": [ + "degree", + "freq" + ], + "defaultValue": "degree", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "display_empty_intersections", + "displayName": "Display Empty Intersections", + "description": "If FALSE (default) empty sets are not plotted", + "paramType": "BOOLEAN", + "paramGroup": "Intersection Plot", + "paramValues": null, + "defaultValue": "FALSE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "intersection_bar_color", + "displayName": "Intersection Bar Color", + "description": "", + "paramType": "SELECT", + "paramGroup": "Intersection Plot", + "paramValues": [ + "steelblue4", + "aquamarine3", + "salmon1", + "lightskyblue3", + "plum3", + "darkolivegreen3", + "goldenrod1", + "burlywood2", + "gray70", + "firebrick2", + "steelblue", + "palegreen4", + "orchid4", + "darkorange1", + "yellow", + "sienna", + "palevioletred1", + "gray60", + "cyan4", + "darkorange3", + "mediumpurple3", + "violetred2", + "olivedrab", + "darkgoldenrod2", + "darkgoldenrod", + "gray40", + "palegreen3", + "thistle3", + "khaki1", + "deeppink2", + "chocolate3", + "paleturquoise3", + "wheat1", + "lightsteelblue", + "salmon", + "sandybrown", + "darkolivegreen2", + "thistle2", + "gray85", + "orchid3", + "darkseagreen1", + "lightgoldenrod1", + "lightskyblue2", + "dodgerblue3", + "darkseagreen3", + "forestgreen", + "lightpink2", + "mediumpurple4", + "lightpink1", + "thistle", + "navajowhite", + "lemonchiffon", + "bisque2", + "mistyrose", + "gray95", + "lightcyan3", + "peachpuff2", + "lightsteelblue2", + "lightyellow2", + "moccasin", + "antiquewhite2", + "gray80", + "lightgrey" + ], + "defaultValue": "steelblue4", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "intersection_line_width", + "displayName": "Intersection Line Width", + "description": "", + "paramType": "NUMBER", + "paramGroup": "Intersection Plot", + "paramValues": null, + "defaultValue": "0.7", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "intersection_point_size", + "displayName": "Intersection Point Size", + "description": "", + "paramType": "NUMBER", + "paramGroup": "Intersection Plot", + "paramValues": null, + "defaultValue": "2.2", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "table_font_size", + "displayName": "Table Font Size", + "description": "", + "paramType": "NUMBER", + "paramGroup": "Table", + "paramValues": null, + "defaultValue": "0.7", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "table_content", + "displayName": "Table Content", + "description": "", + "paramType": "SELECT", + "paramGroup": "Table", + "paramValues": [ + "all intersections", + "returned intersections" + ], + "defaultValue": "all intersections", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "dpi", + "displayName": "Image Resolution", + "description": "", + "paramType": "NUMBER", + "paramGroup": "Image", + "paramValues": null, + "defaultValue": "300", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "image_height", + "displayName": "Image Height", + "description": "", + "paramType": "NUMBER", + "paramGroup": "Image", + "paramValues": null, + "defaultValue": "3000", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "image_width", + "displayName": "Image Width", + "description": "", + "paramType": "NUMBER", + "paramGroup": "Image", + "paramValues": null, + "defaultValue": "4000", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "save_plots", + "displayName": "Save Plots", + "description": "If this is `TRUE`, any plots generated during the analysis will be saved to disk.", + "paramType": "BOOLEAN", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "outputDatasetName": "Venn Diagram", + "outputs": { + "DataFrame": { + "type": "file", + "name": "venn_diagram_dataframe.rds" + }, + "figures": { + "type": "file", + "name": "figures/diff/venn_diagram.png" + } + } +} \ No newline at end of file diff --git a/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/plot_volcano_enhanced.json b/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/plot_volcano_enhanced.json new file mode 100644 index 0000000..0ce898a --- /dev/null +++ b/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/plot_volcano_enhanced.json @@ -0,0 +1,331 @@ +{ + "title": "Plot Volcano - Enhanced", + "description": "Implementation of Bioconductor's Enhanced Volcano Plot (v1.6.0, https://bioconductor.org/packages/release/bioc/html/EnhancedVolcano.html). Template written by Matthew Angel and maintained by CCBR. Final Potomac Compatible Version: v52. Final Sugarloaf V1 Version: v55. Latest Sugarloaf V2 Version: v67. [View Documentation](https://nidap.nih.gov/workspace/notepad/view/ri.notepad.main.notepad.8fe3cd6c-db24-4b0a-b717-060cb77ecc5e)", + "r_function": "plot_volcano_enhanced", + "columns": [ + { + "key": "feature_id_colname", + "displayName": "Column with Feature ID", + "description": "Column from the input DEG table containing Feature ID (such as Gene Names, Isoform IDs, UniProt IDs, and so on). This is usually the first column (named \"Feature_ID\" or \"Gene\"). Only Text type columns will be allowed.", + "paramGroup": "Basic", + "sourceDataset": "DEG_Table", + "defaultValue": null, + "columnType": "STRING", + "isMulti": null + }, + { + "key": "signif_colname", + "displayName": "Significance Column", + "description": "Choose an unadjusted or adjusted p-value column from the input DEG table to use as the measure of significance in your Volcano plot. If your DEG analysis contained more than one contrast comparison, you will only be able to select one of these at a time. Make sure you select the same contrast that was selected for the \"Log2 Fold Change Column\" parameter.", + "paramGroup": "Basic", + "sourceDataset": "DEG_Table", + "defaultValue": null, + "columnType": "NUMBER", + "isMulti": true + }, + { + "key": "change_colname", + "displayName": "Log2 Fold Change Column", + "description": "Choose a log2 fold change column from the input DEG table. If your DEG analysis contained more than one contrast comparison, you will only be able to select one of these at a time. Make sure you select the same contrast that was selected for the \"Significance Column\" parameter.", + "paramGroup": "Basic", + "sourceDataset": "DEG_Table", + "defaultValue": null, + "columnType": "NUMBER", + "isMulti": true + } + ], + "inputDatasets": [ + { + "key": "moo_input_rds", + "displayName": "MOO input Rds", + "description": "File path to read the input multiOmicDataSet object (MOO)", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "parameters": [ + { + "key": "moo_output_rds", + "displayName": "Summary dataframe output Rds", + "description": "File path to the summary dataframe as an Rds file", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "enhanced_volcano_plot.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "signif_threshold", + "displayName": "P-Value Threshold", + "description": "", + "paramType": "NUMBER", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": "0.001", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "change_threshold", + "displayName": "Log2 Fold Change Threshold", + "description": "", + "paramType": "NUMBER", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": "1.0", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "value_to_sort_the_output_dataset", + "displayName": "How to sort the output dataset", + "description": "This selection determines how the feature (gene) list is sorted before choosing the top-N features as set by the \"Number of Features to Label\" parameter. Choose either (absolute) fold change, p-value, or t-statistic to label the top features by the selected metric. This also determines which features are labeled in the plot. This option is negated if only using custom labels.", + "paramType": "SELECT", + "paramGroup": "Label", + "paramValues": [ + "p-value", + "fold-change" + ], + "defaultValue": "p-value", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "num_features_to_label", + "displayName": "Number of Features to Label", + "description": "To minimize clutter on the volcano plot, it is inadvisable to label every feature (gene). You can choose to label any number of features or none. The value of this parameter (N) is used to label the top N features only. See the \"Choose Features To Label By\" parameter for options on how to sort the gene list before labeling the top N features. Will be negated if the option to use only additional labels is selected.", + "paramType": "NUMBER", + "paramGroup": "Label", + "paramValues": null, + "defaultValue": "30", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "use_only_addition_labels", + "displayName": "Label Only My Feature List", + "description": "Select TRUE when you want to label ONLY a specific list of features given in the \"My Feature List\" parameter.", + "paramType": "BOOLEAN", + "paramGroup": "Label", + "paramValues": null, + "defaultValue": "FALSE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "additional_labels", + "displayName": "My Feature List", + "description": "Additional features (genes) to label. If the option to use only custom labels is selected, these will be the only points labeled on the plot. Otherwise, these will be plotted in addition to the other top features. This should be a comma-separated or space-delimited list.", + "paramType": "STRING", + "paramGroup": "Label", + "paramValues": null, + "defaultValue": "", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "lab_size", + "displayName": "Label Size", + "description": "", + "paramType": "NUMBER", + "paramGroup": "Label", + "paramValues": null, + "defaultValue": "4", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "change_sig_name", + "displayName": "Custom Significance Label", + "description": "This replaces bulky names for the p-value column.", + "paramType": "STRING", + "paramGroup": "Title and Axis labels", + "paramValues": null, + "defaultValue": "p-value", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "change_lfc_name", + "displayName": "Custom Log Fold Change Label", + "description": "This replaces bulky column names for the fold-change column.", + "paramType": "STRING", + "paramGroup": "Title and Axis labels", + "paramValues": null, + "defaultValue": "log2FC", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "use_custom_lab", + "displayName": "Use Custom Labels", + "description": "", + "paramType": "BOOLEAN", + "paramGroup": "Title and Axis Labels", + "paramValues": null, + "defaultValue": false, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "title", + "displayName": "Plot Title", + "description": "", + "paramType": "STRING", + "paramGroup": "Title and Axis labels", + "paramValues": null, + "defaultValue": "Volcano Plots", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "ylim", + "displayName": "Y-Limit", + "description": "Maximum value for y-axis. Defaults to -log10(min(pval)). Set to 0 for automatic scaling.", + "paramType": "NUMBER", + "paramGroup": "Plot", + "paramValues": null, + "defaultValue": "0", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "custom_xlim", + "displayName": "Custom X-axis limits", + "description": "Leave empty for automatic scaling, put one number for symmetrical scale (i.e, putting \"5\" would result in a range from \"-5\" to \"5\"), or put two numbers separated by comma for \"asymmetrical\" scale (i.e, putting \"-2,4\" would result in a range from \"-2\" to \"4\")", + "paramType": "STRING", + "paramGroup": "Plot", + "paramValues": null, + "defaultValue": "", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "xlim_additional", + "displayName": "X-Limit Padding", + "description": "Add additional units to x-limit", + "paramType": "NUMBER", + "paramGroup": "Plot", + "paramValues": null, + "defaultValue": "0", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "ylim_additional", + "displayName": "Y-Limit Padding", + "description": "Adds additional units to y-limit.", + "paramType": "NUMBER", + "paramGroup": "Plot", + "paramValues": null, + "defaultValue": "0", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "axis_lab_size", + "displayName": "Axis Label Size", + "description": "", + "paramType": "NUMBER", + "paramGroup": "Plot", + "paramValues": null, + "defaultValue": "24", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "point_size", + "displayName": "Point Size", + "description": "", + "paramType": "NUMBER", + "paramGroup": "Plot", + "paramValues": null, + "defaultValue": "2", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "image_width", + "displayName": "Image Width", + "description": "", + "paramType": "NUMBER", + "paramGroup": "Image", + "paramValues": null, + "defaultValue": "3000", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "image_height", + "displayName": "Image Height", + "description": "", + "paramType": "NUMBER", + "paramGroup": "Image", + "paramValues": null, + "defaultValue": "3000", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "dpi", + "displayName": "Image Resolution (DPI)", + "description": "", + "paramType": "NUMBER", + "paramGroup": "Image", + "paramValues": null, + "defaultValue": "300", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "save_plots", + "displayName": "Save Plots", + "description": "If this is `TRUE`, any plots generated during the analysis will be saved to disk.", + "paramType": "BOOLEAN", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "outputDatasetName": "Volcano Plot - Enhanced", + "outputs": { + "DataFrame": { + "type": "file", + "name": "enhanced_volcano_dataframe.rds" + }, + "figures": { + "type": "file", + "name": "figures/diff/volcano_enhanced.png" + } + } +} \ No newline at end of file diff --git a/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/plot_volcano_summary.json b/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/plot_volcano_summary.json new file mode 100644 index 0000000..2d411a5 --- /dev/null +++ b/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/plot_volcano_summary.json @@ -0,0 +1,5125 @@ +{ + "title": "Plot Volcano - Summary", + "description": "Produces one volcano plot for each tested contrast in the input DEG table.\n\nIt can be sorted by either fold change, t-statistic, or p-value. The returned dataset includes one row for each significant gene in each contrast, and contains columns from the DEG analysis of that contrast as well as columns useful to the Venn diagram template downstream.", + "r_function": "plot_volcano_summary", + "columns": [ + { + "key": "feature_id_colname", + "displayName": "Gene Names Column", + "description": "The column from your input DEG table containing the gene names. This is usually the first column. Only columns of Text type from your DEG table will be available to select for this parameter.", + "paramGroup": "Basic", + "sourceDataset": "DEG_Table", + "defaultValue": null, + "columnType": "STRING", + "isMulti": null + } + ], + "inputDatasets": [ + { + "key": "moo_input_rds", + "displayName": "MOO input Rds", + "description": "File path to read the input multiOmicDataSet object (MOO)", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "parameters": [ + { + "key": "moo_output_rds", + "displayName": "Summary dataframe output Rds", + "description": "File path to output summary data as an Rds file", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "signif_colname", + "displayName": "Significance column name", + "description": "Choose whether to use unadjusted or adjusted p-values in the resulting volcano plots.", + "paramType": "SELECT", + "paramGroup": "Basic", + "paramValues": [ + "pval", + "adjpval" + ], + "defaultValue": "pval", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "signif_threshold", + "displayName": "P-Value Threshold", + "description": "Generates a horizontal blue line at -log10 of this value on the y-axis of the volcano plot. Genes located above this threshold are considered significantly differentially expressed.", + "paramType": "NUMBER", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": "0.001", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "change_threshold", + "displayName": "Log2 Fold Change Threshold", + "description": "Generates two vertical red lines at +/- this value on the x-axis of the volcano plot. A value of 1 entered here will draw lines at a log2 fold change values of -1 and 1. This corresponds to unlogged fold changes of 2 and 1/2, respectively.", + "paramType": "NUMBER", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": "1", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "value_to_sort_the_output_dataset", + "displayName": "Choose How to sort the output dataset", + "description": "This selection determines how the gene list is sorted before choosing the top-N genes as set by the \"Number of Genes to Label\" parameter. Choose either (absolute) fold change, p-value, or t-statistic to label the top genes by the selected metric.", + "paramType": "SELECT", + "paramGroup": "Gene Name Label", + "paramValues": [ + "fold-change", + "p-value", + "t-statistic" + ], + "defaultValue": "t-statistic", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "num_features_to_label", + "displayName": "Number of Genes to Label", + "description": "To minimize clutter on the volcano plot, it is inadvisable to label every gene. You can choose to label any number of genes or none. The value of this parameter (N) is used to label the top N genes only. See the \"Choose Genes To Label By\" parameter for options on how to sort the gene list before labeling the top N genes.", + "paramType": "NUMBER", + "paramGroup": "Gene Name Label", + "paramValues": null, + "defaultValue": "30", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "add_features", + "displayName": "Add Custom Features List To Labels", + "description": "Set TRUE when you want to label a specific set of genes in the \"My Gene List\" parameter\" IN ADDITION to the number of genes you set in the \"Number of Genes to Label\" parameter.", + "paramType": "BOOLEAN", + "paramGroup": "Gene Name Label", + "paramValues": null, + "defaultValue": "FALSE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "label_features", + "displayName": "Label Only Custom Features List", + "description": "Select TRUE when you want to label ONLY a specific list of genes given in the \"My Gene List\" parameter.", + "paramType": "BOOLEAN", + "paramGroup": "Gene Name Label", + "paramValues": null, + "defaultValue": "FALSE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "custom_gene_list", + "displayName": "Custom Feature/Gene List", + "description": "Provide a list of genes (comma separated) to be labeled on the volcano plot. You must toggle one of the following ON to see these labels: \"Add My Gene List To Labels\" or \"Label Only My Gene List\".", + "paramType": "STRING", + "paramGroup": "Gene Name Label", + "paramValues": null, + "defaultValue": "Provide list of genes-comma separated", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "default_label_color", + "displayName": "Default Feature Label Text Color", + "description": "Set the color for the text used to add gene name labels to points.", + "paramType": "SELECT", + "paramGroup": "Gene Name Label", + "paramValues": [ + "white", + "aliceblue", + "antiquewhite", + "antiquewhite1", + "antiquewhite2", + "antiquewhite3", + "antiquewhite4", + "aquamarine", + "aquamarine1", + "aquamarine2", + "aquamarine3", + "aquamarine4", + "azure", + "azure1", + "azure2", + "azure3", + "azure4", + "beige", + "bisque", + "bisque1", + "bisque2", + "bisque3", + "bisque4", + "black", + "blanchedalmond", + "blue", + "blue1", + "blue2", + "blue3", + "blue4", + "blueviolet", + "brown", + "brown1", + "brown2", + "brown3", + "brown4", + "burlywood", + "burlywood1", + "burlywood2", + "burlywood3", + "burlywood4", + "cadetblue", + "cadetblue1", + "cadetblue2", + "cadetblue3", + "cadetblue4", + "chartreuse", + "chartreuse1", + "chartreuse2", + "chartreuse3", + "chartreuse4", + "chocolate", + "chocolate1", + "chocolate2", + "chocolate3", + "chocolate4", + "coral", + "coral1", + "coral2", + "coral3", + "coral4", + "cornflowerblue", + "cornsilk", + "cornsilk1", + "cornsilk2", + "cornsilk3", + "cornsilk4", + "cyan", + "cyan1", + "cyan2", + "cyan3", + "cyan4", + "darkblue", + "darkcyan", + "darkgoldenrod", + "darkgoldenrod1", + "darkgoldenrod2", + "darkgoldenrod3", + "darkgoldenrod4", + "darkgray", + "darkgreen", + "darkgrey", + "darkkhaki", + "darkmagenta", + "darkolivegreen", + "darkolivegreen1", + "darkolivegreen2", + "darkolivegreen3", + "darkolivegreen4", + "darkorange", + "darkorange1", + "darkorange2", + "darkorange3", + "darkorange4", + "darkorchid", + "darkorchid1", + "darkorchid2", + "darkorchid3", + "darkorchid4", + "darkred", + "darksalmon", + "darkseagreen", + "darkseagreen1", + "darkseagreen2", + "darkseagreen3", + "darkseagreen4", + "darkslateblue", + "darkslategray", + "darkslategray1", + "darkslategray2", + "darkslategray3", + "darkslategray4", + "darkslategrey", + "darkturquoise", + "darkviolet", + "deeppink", + "deeppink1", + "deeppink2", + "deeppink3", + "deeppink4", + "deepskyblue", + "deepskyblue1", + "deepskyblue2", + "deepskyblue3", + "deepskyblue4", + "dimgray", + "dimgrey", + "dodgerblue", + "dodgerblue1", + "dodgerblue2", + "dodgerblue3", + "dodgerblue4", + "firebrick", + "firebrick1", + "firebrick2", + "firebrick3", + "firebrick4", + "floralwhite", + "forestgreen", + "gainsboro", + "ghostwhite", + "gold", + "gold1", + "gold2", + "gold3", + "gold4", + "goldenrod", + "goldenrod1", + "goldenrod2", + "goldenrod3", + "goldenrod4", + "gray", + "gray0", + "gray1", + "gray2", + "gray3", + "gray4", + "gray5", + "gray6", + "gray7", + "gray8", + "gray9", + "gray10", + "gray11", + "gray12", + "gray13", + "gray14", + "gray15", + "gray16", + "gray17", + "gray18", + "gray19", + "gray20", + "gray21", + "gray22", + "gray23", + "gray24", + "gray25", + "gray26", + "gray27", + "gray28", + "gray29", + "gray30", + "gray31", + "gray32", + "gray33", + "gray34", + "gray35", + "gray36", + "gray37", + "gray38", + "gray39", + "gray40", + "gray41", + "gray42", + "gray43", + "gray44", + "gray45", + "gray46", + "gray47", + "gray48", + "gray49", + "gray50", + "gray51", + "gray52", + "gray53", + "gray54", + "gray55", + "gray56", + "gray57", + "gray58", + "gray59", + "gray60", + "gray61", + "gray62", + "gray63", + "gray64", + "gray65", + "gray66", + "gray67", + "gray68", + "gray69", + "gray70", + "gray71", + "gray72", + "gray73", + "gray74", + "gray75", + "gray76", + "gray77", + "gray78", + "gray79", + "gray80", + "gray81", + "gray82", + "gray83", + "gray84", + "gray85", + "gray86", + "gray87", + "gray88", + "gray89", + "gray90", + "gray91", + "gray92", + "gray93", + "gray94", + "gray95", + "gray96", + "gray97", + "gray98", + "gray99", + "gray100", + "green", + "green1", + "green2", + "green3", + "green4", + "greenyellow", + "grey", + "grey0", + "grey1", + "grey2", + "grey3", + "grey4", + "grey5", + "grey6", + "grey7", + "grey8", + "grey9", + "grey10", + "grey11", + "grey12", + "grey13", + "grey14", + "grey15", + "grey16", + "grey17", + "grey18", + "grey19", + "grey20", + "grey21", + "grey22", + "grey23", + "grey24", + "grey25", + "grey26", + "grey27", + "grey28", + "grey29", + "grey30", + "grey31", + "grey32", + "grey33", + "grey34", + "grey35", + "grey36", + "grey37", + "grey38", + "grey39", + "grey40", + "grey41", + "grey42", + "grey43", + "grey44", + "grey45", + "grey46", + "grey47", + "grey48", + "grey49", + "grey50", + "grey51", + "grey52", + "grey53", + "grey54", + "grey55", + "grey56", + "grey57", + "grey58", + "grey59", + "grey60", + "grey61", + "grey62", + "grey63", + "grey64", + "grey65", + "grey66", + "grey67", + "grey68", + "grey69", + "grey70", + "grey71", + "grey72", + "grey73", + "grey74", + "grey75", + "grey76", + "grey77", + "grey78", + "grey79", + "grey80", + "grey81", + "grey82", + "grey83", + "grey84", + "grey85", + "grey86", + "grey87", + "grey88", + "grey89", + "grey90", + "grey91", + "grey92", + "grey93", + "grey94", + "grey95", + "grey96", + "grey97", + "grey98", + "grey99", + "grey100", + "honeydew", + "honeydew1", + "honeydew2", + "honeydew3", + "honeydew4", + "hotpink", + "hotpink1", + "hotpink2", + "hotpink3", + "hotpink4", + "indianred", + "indianred1", + "indianred2", + "indianred3", + "indianred4", + "ivory", + "ivory1", + "ivory2", + "ivory3", + "ivory4", + "khaki", + "khaki1", + "khaki2", + "khaki3", + "khaki4", + "lavender", + "lavenderblush", + "lavenderblush1", + "lavenderblush2", + "lavenderblush3", + "lavenderblush4", + "lawngreen", + "lemonchiffon", + "lemonchiffon1", + "lemonchiffon2", + "lemonchiffon3", + "lemonchiffon4", + "lightblue", + "lightblue1", + "lightblue2", + "lightblue3", + "lightblue4", + "lightcoral", + "lightcyan", + "lightcyan1", + "lightcyan2", + "lightcyan3", + "lightcyan4", + "lightgoldenrod", + "lightgoldenrod1", + "lightgoldenrod2", + "lightgoldenrod3", + "lightgoldenrod4", + "lightgoldenrodyellow", + "lightgray", + "lightgreen", + "lightgrey", + "lightpink", + "lightpink1", + "lightpink2", + "lightpink3", + "lightpink4", + "lightsalmon", + "lightsalmon1", + "lightsalmon2", + "lightsalmon3", + "lightsalmon4", + "lightseagreen", + "lightskyblue", + "lightskyblue1", + "lightskyblue2", + "lightskyblue3", + "lightskyblue4", + "lightslateblue", + "lightslategray", + "lightslategrey", + "lightsteelblue", + "lightsteelblue1", + "lightsteelblue2", + "lightsteelblue3", + "lightsteelblue4", + "lightyellow", + "lightyellow1", + "lightyellow2", + "lightyellow3", + "lightyellow4", + "limegreen", + "linen", + "magenta", + "magenta1", + "magenta2", + "magenta3", + "magenta4", + "maroon", + "maroon1", + "maroon2", + "maroon3", + "maroon4", + "mediumaquamarine", + "mediumblue", + "mediumorchid", + "mediumorchid1", + "mediumorchid2", + "mediumorchid3", + "mediumorchid4", + "mediumpurple", + "mediumpurple1", + "mediumpurple2", + "mediumpurple3", + "mediumpurple4", + "mediumseagreen", + "mediumslateblue", + "mediumspringgreen", + "mediumturquoise", + "mediumvioletred", + "midnightblue", + "mintcream", + "mistyrose", + "mistyrose1", + "mistyrose2", + "mistyrose3", + "mistyrose4", + "moccasin", + "navajowhite", + "navajowhite1", + "navajowhite2", + "navajowhite3", + "navajowhite4", + "navy", + "navyblue", + "oldlace", + "olivedrab", + "olivedrab1", + "olivedrab2", + "olivedrab3", + "olivedrab4", + "orange", + "orange1", + "orange2", + "orange3", + "orange4", + "orangered", + "orangered1", + "orangered2", + "orangered3", + "orangered4", + "orchid", + "orchid1", + "orchid2", + "orchid3", + "orchid4", + "palegoldenrod", + "palegreen", + "palegreen1", + "palegreen2", + "palegreen3", + "palegreen4", + "paleturquoise", + "paleturquoise1", + "paleturquoise2", + "paleturquoise3", + "paleturquoise4", + "palevioletred", + "palevioletred1", + "palevioletred2", + "palevioletred3", + "palevioletred4", + "papayawhip", + "peachpuff", + "peachpuff1", + "peachpuff2", + "peachpuff3", + "peachpuff4", + "peru", + "pink", + "pink1", + "pink2", + "pink3", + "pink4", + "plum", + "plum1", + "plum2", + "plum3", + "plum4", + "powderblue", + "purple", + "purple1", + "purple2", + "purple3", + "purple4", + "red", + "red1", + "red2", + "red3", + "red4", + "rosybrown", + "rosybrown1", + "rosybrown2", + "rosybrown3", + "rosybrown4", + "royalblue", + "royalblue1", + "royalblue2", + "royalblue3", + "royalblue4", + "saddlebrown", + "salmon", + "salmon1", + "salmon2", + "salmon3", + "salmon4", + "sandybrown", + "seagreen", + "seagreen1", + "seagreen2", + "seagreen3", + "seagreen4", + "seashell", + "seashell1", + "seashell2", + "seashell3", + "seashell4", + "sienna", + "sienna1", + "sienna2", + "sienna3", + "sienna4", + "skyblue", + "skyblue1", + "skyblue2", + "skyblue3", + "skyblue4", + "slateblue", + "slateblue1", + "slateblue2", + "slateblue3", + "slateblue4", + "slategray", + "slategray1", + "slategray2", + "slategray3", + "slategray4", + "slategrey", + "snow", + "snow1", + "snow2", + "snow3", + "snow4", + "springgreen", + "springgreen1", + "springgreen2", + "springgreen3", + "springgreen4", + "steelblue", + "steelblue1", + "steelblue2", + "steelblue3", + "steelblue4", + "tan", + "tan1", + "tan2", + "tan3", + "tan4", + "thistle", + "thistle1", + "thistle2", + "thistle3", + "thistle4", + "tomato", + "tomato1", + "tomato2", + "tomato3", + "tomato4", + "turquoise", + "turquoise1", + "turquoise2", + "turquoise3", + "turquoise4", + "violet", + "violetred", + "violetred1", + "violetred2", + "violetred3", + "violetred4", + "wheat", + "wheat1", + "wheat2", + "wheat3", + "wheat4", + "whitesmoke", + "yellow", + "yellow1", + "yellow2", + "yellow3", + "yellow4", + "yellowgreen" + ], + "defaultValue": "black", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "custom_label_color", + "displayName": "Feature Label Text Color for custom features list", + "description": "Set the color for the specific list of genes provided in the \"Gene List\" parameter.", + "paramType": "SELECT", + "paramGroup": "Gene Name Label", + "paramValues": [ + "white", + "aliceblue", + "antiquewhite", + "antiquewhite1", + "antiquewhite2", + "antiquewhite3", + "antiquewhite4", + "aquamarine", + "aquamarine1", + "aquamarine2", + "aquamarine3", + "aquamarine4", + "azure", + "azure1", + "azure2", + "azure3", + "azure4", + "beige", + "bisque", + "bisque1", + "bisque2", + "bisque3", + "bisque4", + "black", + "blanchedalmond", + "blue", + "blue1", + "blue2", + "blue3", + "blue4", + "blueviolet", + "brown", + "brown1", + "brown2", + "brown3", + "brown4", + "burlywood", + "burlywood1", + "burlywood2", + "burlywood3", + "burlywood4", + "cadetblue", + "cadetblue1", + "cadetblue2", + "cadetblue3", + "cadetblue4", + "chartreuse", + "chartreuse1", + "chartreuse2", + "chartreuse3", + "chartreuse4", + "chocolate", + "chocolate1", + "chocolate2", + "chocolate3", + "chocolate4", + "coral", + "coral1", + "coral2", + "coral3", + "coral4", + "cornflowerblue", + "cornsilk", + "cornsilk1", + "cornsilk2", + "cornsilk3", + "cornsilk4", + "cyan", + "cyan1", + "cyan2", + "cyan3", + "cyan4", + "darkblue", + "darkcyan", + "darkgoldenrod", + "darkgoldenrod1", + "darkgoldenrod2", + "darkgoldenrod3", + "darkgoldenrod4", + "darkgray", + "darkgreen", + "darkgrey", + "darkkhaki", + "darkmagenta", + "darkolivegreen", + "darkolivegreen1", + "darkolivegreen2", + "darkolivegreen3", + "darkolivegreen4", + "darkorange", + "darkorange1", + "darkorange2", + "darkorange3", + "darkorange4", + "darkorchid", + "darkorchid1", + "darkorchid2", + "darkorchid3", + "darkorchid4", + "darkred", + "darksalmon", + "darkseagreen", + "darkseagreen1", + "darkseagreen2", + "darkseagreen3", + "darkseagreen4", + "darkslateblue", + "darkslategray", + "darkslategray1", + "darkslategray2", + "darkslategray3", + "darkslategray4", + "darkslategrey", + "darkturquoise", + "darkviolet", + "deeppink", + "deeppink1", + "deeppink2", + "deeppink3", + "deeppink4", + "deepskyblue", + "deepskyblue1", + "deepskyblue2", + "deepskyblue3", + "deepskyblue4", + "dimgray", + "dimgrey", + "dodgerblue", + "dodgerblue1", + "dodgerblue2", + "dodgerblue3", + "dodgerblue4", + "firebrick", + "firebrick1", + "firebrick2", + "firebrick3", + "firebrick4", + "floralwhite", + "forestgreen", + "gainsboro", + "ghostwhite", + "gold", + "gold1", + "gold2", + "gold3", + "gold4", + "goldenrod", + "goldenrod1", + "goldenrod2", + "goldenrod3", + "goldenrod4", + "gray", + "gray0", + "gray1", + "gray2", + "gray3", + "gray4", + "gray5", + "gray6", + "gray7", + "gray8", + "gray9", + "gray10", + "gray11", + "gray12", + "gray13", + "gray14", + "gray15", + "gray16", + "gray17", + "gray18", + "gray19", + "gray20", + "gray21", + "gray22", + "gray23", + "gray24", + "gray25", + "gray26", + "gray27", + "gray28", + "gray29", + "gray30", + "gray31", + "gray32", + "gray33", + "gray34", + "gray35", + "gray36", + "gray37", + "gray38", + "gray39", + "gray40", + "gray41", + "gray42", + "gray43", + "gray44", + "gray45", + "gray46", + "gray47", + "gray48", + "gray49", + "gray50", + "gray51", + "gray52", + "gray53", + "gray54", + "gray55", + "gray56", + "gray57", + "gray58", + "gray59", + "gray60", + "gray61", + "gray62", + "gray63", + "gray64", + "gray65", + "gray66", + "gray67", + "gray68", + "gray69", + "gray70", + "gray71", + "gray72", + "gray73", + "gray74", + "gray75", + "gray76", + "gray77", + "gray78", + "gray79", + "gray80", + "gray81", + "gray82", + "gray83", + "gray84", + "gray85", + "gray86", + "gray87", + "gray88", + "gray89", + "gray90", + "gray91", + "gray92", + "gray93", + "gray94", + "gray95", + "gray96", + "gray97", + "gray98", + "gray99", + "gray100", + "green", + "green1", + "green2", + "green3", + "green4", + "greenyellow", + "grey", + "grey0", + "grey1", + "grey2", + "grey3", + "grey4", + "grey5", + "grey6", + "grey7", + "grey8", + "grey9", + "grey10", + "grey11", + "grey12", + "grey13", + "grey14", + "grey15", + "grey16", + "grey17", + "grey18", + "grey19", + "grey20", + "grey21", + "grey22", + "grey23", + "grey24", + "grey25", + "grey26", + "grey27", + "grey28", + "grey29", + "grey30", + "grey31", + "grey32", + "grey33", + "grey34", + "grey35", + "grey36", + "grey37", + "grey38", + "grey39", + "grey40", + "grey41", + "grey42", + "grey43", + "grey44", + "grey45", + "grey46", + "grey47", + "grey48", + "grey49", + "grey50", + "grey51", + "grey52", + "grey53", + "grey54", + "grey55", + "grey56", + "grey57", + "grey58", + "grey59", + "grey60", + "grey61", + "grey62", + "grey63", + "grey64", + "grey65", + "grey66", + "grey67", + "grey68", + "grey69", + "grey70", + "grey71", + "grey72", + "grey73", + "grey74", + "grey75", + "grey76", + "grey77", + "grey78", + "grey79", + "grey80", + "grey81", + "grey82", + "grey83", + "grey84", + "grey85", + "grey86", + "grey87", + "grey88", + "grey89", + "grey90", + "grey91", + "grey92", + "grey93", + "grey94", + "grey95", + "grey96", + "grey97", + "grey98", + "grey99", + "grey100", + "honeydew", + "honeydew1", + "honeydew2", + "honeydew3", + "honeydew4", + "hotpink", + "hotpink1", + "hotpink2", + "hotpink3", + "hotpink4", + "indianred", + "indianred1", + "indianred2", + "indianred3", + "indianred4", + "ivory", + "ivory1", + "ivory2", + "ivory3", + "ivory4", + "khaki", + "khaki1", + "khaki2", + "khaki3", + "khaki4", + "lavender", + "lavenderblush", + "lavenderblush1", + "lavenderblush2", + "lavenderblush3", + "lavenderblush4", + "lawngreen", + "lemonchiffon", + "lemonchiffon1", + "lemonchiffon2", + "lemonchiffon3", + "lemonchiffon4", + "lightblue", + "lightblue1", + "lightblue2", + "lightblue3", + "lightblue4", + "lightcoral", + "lightcyan", + "lightcyan1", + "lightcyan2", + "lightcyan3", + "lightcyan4", + "lightgoldenrod", + "lightgoldenrod1", + "lightgoldenrod2", + "lightgoldenrod3", + "lightgoldenrod4", + "lightgoldenrodyellow", + "lightgray", + "lightgreen", + "lightgrey", + "lightpink", + "lightpink1", + "lightpink2", + "lightpink3", + "lightpink4", + "lightsalmon", + "lightsalmon1", + "lightsalmon2", + "lightsalmon3", + "lightsalmon4", + "lightseagreen", + "lightskyblue", + "lightskyblue1", + "lightskyblue2", + "lightskyblue3", + "lightskyblue4", + "lightslateblue", + "lightslategray", + "lightslategrey", + "lightsteelblue", + "lightsteelblue1", + "lightsteelblue2", + "lightsteelblue3", + "lightsteelblue4", + "lightyellow", + "lightyellow1", + "lightyellow2", + "lightyellow3", + "lightyellow4", + "limegreen", + "linen", + "magenta", + "magenta1", + "magenta2", + "magenta3", + "magenta4", + "maroon", + "maroon1", + "maroon2", + "maroon3", + "maroon4", + "mediumaquamarine", + "mediumblue", + "mediumorchid", + "mediumorchid1", + "mediumorchid2", + "mediumorchid3", + "mediumorchid4", + "mediumpurple", + "mediumpurple1", + "mediumpurple2", + "mediumpurple3", + "mediumpurple4", + "mediumseagreen", + "mediumslateblue", + "mediumspringgreen", + "mediumturquoise", + "mediumvioletred", + "midnightblue", + "mintcream", + "mistyrose", + "mistyrose1", + "mistyrose2", + "mistyrose3", + "mistyrose4", + "moccasin", + "navajowhite", + "navajowhite1", + "navajowhite2", + "navajowhite3", + "navajowhite4", + "navy", + "navyblue", + "oldlace", + "olivedrab", + "olivedrab1", + "olivedrab2", + "olivedrab3", + "olivedrab4", + "orange", + "orange1", + "orange2", + "orange3", + "orange4", + "orangered", + "orangered1", + "orangered2", + "orangered3", + "orangered4", + "orchid", + "orchid1", + "orchid2", + "orchid3", + "orchid4", + "palegoldenrod", + "palegreen", + "palegreen1", + "palegreen2", + "palegreen3", + "palegreen4", + "paleturquoise", + "paleturquoise1", + "paleturquoise2", + "paleturquoise3", + "paleturquoise4", + "palevioletred", + "palevioletred1", + "palevioletred2", + "palevioletred3", + "palevioletred4", + "papayawhip", + "peachpuff", + "peachpuff1", + "peachpuff2", + "peachpuff3", + "peachpuff4", + "peru", + "pink", + "pink1", + "pink2", + "pink3", + "pink4", + "plum", + "plum1", + "plum2", + "plum3", + "plum4", + "powderblue", + "purple", + "purple1", + "purple2", + "purple3", + "purple4", + "red", + "red1", + "red2", + "red3", + "red4", + "rosybrown", + "rosybrown1", + "rosybrown2", + "rosybrown3", + "rosybrown4", + "royalblue", + "royalblue1", + "royalblue2", + "royalblue3", + "royalblue4", + "saddlebrown", + "salmon", + "salmon1", + "salmon2", + "salmon3", + "salmon4", + "sandybrown", + "seagreen", + "seagreen1", + "seagreen2", + "seagreen3", + "seagreen4", + "seashell", + "seashell1", + "seashell2", + "seashell3", + "seashell4", + "sienna", + "sienna1", + "sienna2", + "sienna3", + "sienna4", + "skyblue", + "skyblue1", + "skyblue2", + "skyblue3", + "skyblue4", + "slateblue", + "slateblue1", + "slateblue2", + "slateblue3", + "slateblue4", + "slategray", + "slategray1", + "slategray2", + "slategray3", + "slategray4", + "slategrey", + "snow", + "snow1", + "snow2", + "snow3", + "snow4", + "springgreen", + "springgreen1", + "springgreen2", + "springgreen3", + "springgreen4", + "steelblue", + "steelblue1", + "steelblue2", + "steelblue3", + "steelblue4", + "tan", + "tan1", + "tan2", + "tan3", + "tan4", + "thistle", + "thistle1", + "thistle2", + "thistle3", + "thistle4", + "tomato", + "tomato1", + "tomato2", + "tomato3", + "tomato4", + "turquoise", + "turquoise1", + "turquoise2", + "turquoise3", + "turquoise4", + "violet", + "violetred", + "violetred1", + "violetred2", + "violetred3", + "violetred4", + "wheat", + "wheat1", + "wheat2", + "wheat3", + "wheat4", + "whitesmoke", + "yellow", + "yellow1", + "yellow2", + "yellow3", + "yellow4", + "yellowgreen" + ], + "defaultValue": "green3", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "label_x_adj", + "displayName": "Label Position Adjustment (X-Axis)", + "description": "", + "paramType": "NUMBER", + "paramGroup": "Gene Name Label", + "paramValues": null, + "defaultValue": "0.2", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "label_y_adj", + "displayName": "Label Position Adjustment (Y-Axis)", + "description": "", + "paramType": "NUMBER", + "paramGroup": "Gene Name Label", + "paramValues": null, + "defaultValue": "0.2", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "line_thickness", + "displayName": "Line Segment Thickness", + "description": "Thickness of the line connecting the point and it's gene label", + "paramType": "NUMBER", + "paramGroup": "Gene Name Label", + "paramValues": null, + "defaultValue": "0.5", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "label_font_size", + "displayName": "Label Font Size", + "description": "Font size for sample labels. Set to 0 to remove labels.", + "paramType": "NUMBER", + "paramGroup": "Gene Name Label", + "paramValues": null, + "defaultValue": 4, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "label_font_type", + "displayName": "Label Font Type", + "description": "Select the font type for the gene labels displayed in the volcano plot. The options are: 1-regular, 2-bold, 3-italic, 4-bold.italic, 5-greek alphabet.", + "paramType": "NUMBER", + "paramGroup": "Gene Name Label", + "paramValues": null, + "defaultValue": "1", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "displace_feature_labels", + "displayName": "Displace Feature Labels", + "description": "Set TRUE if you want to displace the gene label for a specific set of genes. Make sure to use custom x- and y- limits and give sufficient space for displacement; otherwise other labels than the desired ones will appear displaced.", + "paramType": "BOOLEAN", + "paramGroup": "Gene Name Label", + "paramValues": null, + "defaultValue": "FALSE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "custom_gene_list_special_label_displacement", + "displayName": "Gene List Special Label Displacement", + "description": "Provide a list of features (comma separated) for which you want special displacement of the gene label.", + "paramType": "STRING", + "paramGroup": "Gene Name Label", + "paramValues": null, + "defaultValue": "Provide list of genes-comma separated", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "special_label_displacement_x_axis", + "displayName": "Special Label Displacement (X-Axis)", + "description": "Choose a number to set the nudge/displacement of the gene label in the x-direction.", + "paramType": "NUMBER", + "paramGroup": "Gene Name Label", + "paramValues": null, + "defaultValue": "2", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "special_label_displacement_y_axis", + "displayName": "Special Label Displacement (Y-Axis)", + "description": "Choose a number (comma separated) to set the nudge/displacement of the gene label in the x-direction.", + "paramType": "NUMBER", + "paramGroup": "Gene Name Label", + "paramValues": null, + "defaultValue": "2", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "color_of_signif_threshold_line", + "displayName": "Color of P-Value Threshold Line", + "description": "The color of the horizontal p-value threshold line", + "paramType": "SELECT", + "paramGroup": "Plot", + "paramValues": [ + "white", + "aliceblue", + "antiquewhite", + "antiquewhite1", + "antiquewhite2", + "antiquewhite3", + "antiquewhite4", + "aquamarine", + "aquamarine1", + "aquamarine2", + "aquamarine3", + "aquamarine4", + "azure", + "azure1", + "azure2", + "azure3", + "azure4", + "beige", + "bisque", + "bisque1", + "bisque2", + "bisque3", + "bisque4", + "black", + "blanchedalmond", + "blue", + "blue1", + "blue2", + "blue3", + "blue4", + "blueviolet", + "brown", + "brown1", + "brown2", + "brown3", + "brown4", + "burlywood", + "burlywood1", + "burlywood2", + "burlywood3", + "burlywood4", + "cadetblue", + "cadetblue1", + "cadetblue2", + "cadetblue3", + "cadetblue4", + "chartreuse", + "chartreuse1", + "chartreuse2", + "chartreuse3", + "chartreuse4", + "chocolate", + "chocolate1", + "chocolate2", + "chocolate3", + "chocolate4", + "coral", + "coral1", + "coral2", + "coral3", + "coral4", + "cornflowerblue", + "cornsilk", + "cornsilk1", + "cornsilk2", + "cornsilk3", + "cornsilk4", + "cyan", + "cyan1", + "cyan2", + "cyan3", + "cyan4", + "darkblue", + "darkcyan", + "darkgoldenrod", + "darkgoldenrod1", + "darkgoldenrod2", + "darkgoldenrod3", + "darkgoldenrod4", + "darkgray", + "darkgreen", + "darkgrey", + "darkkhaki", + "darkmagenta", + "darkolivegreen", + "darkolivegreen1", + "darkolivegreen2", + "darkolivegreen3", + "darkolivegreen4", + "darkorange", + "darkorange1", + "darkorange2", + "darkorange3", + "darkorange4", + "darkorchid", + "darkorchid1", + "darkorchid2", + "darkorchid3", + "darkorchid4", + "darkred", + "darksalmon", + "darkseagreen", + "darkseagreen1", + "darkseagreen2", + "darkseagreen3", + "darkseagreen4", + "darkslateblue", + "darkslategray", + "darkslategray1", + "darkslategray2", + "darkslategray3", + "darkslategray4", + "darkslategrey", + "darkturquoise", + "darkviolet", + "deeppink", + "deeppink1", + "deeppink2", + "deeppink3", + "deeppink4", + "deepskyblue", + "deepskyblue1", + "deepskyblue2", + "deepskyblue3", + "deepskyblue4", + "dimgray", + "dimgrey", + "dodgerblue", + "dodgerblue1", + "dodgerblue2", + "dodgerblue3", + "dodgerblue4", + "firebrick", + "firebrick1", + "firebrick2", + "firebrick3", + "firebrick4", + "floralwhite", + "forestgreen", + "gainsboro", + "ghostwhite", + "gold", + "gold1", + "gold2", + "gold3", + "gold4", + "goldenrod", + "goldenrod1", + "goldenrod2", + "goldenrod3", + "goldenrod4", + "gray", + "gray0", + "gray1", + "gray2", + "gray3", + "gray4", + "gray5", + "gray6", + "gray7", + "gray8", + "gray9", + "gray10", + "gray11", + "gray12", + "gray13", + "gray14", + "gray15", + "gray16", + "gray17", + "gray18", + "gray19", + "gray20", + "gray21", + "gray22", + "gray23", + "gray24", + "gray25", + "gray26", + "gray27", + "gray28", + "gray29", + "gray30", + "gray31", + "gray32", + "gray33", + "gray34", + "gray35", + "gray36", + "gray37", + "gray38", + "gray39", + "gray40", + "gray41", + "gray42", + "gray43", + "gray44", + "gray45", + "gray46", + "gray47", + "gray48", + "gray49", + "gray50", + "gray51", + "gray52", + "gray53", + "gray54", + "gray55", + "gray56", + "gray57", + "gray58", + "gray59", + "gray60", + "gray61", + "gray62", + "gray63", + "gray64", + "gray65", + "gray66", + "gray67", + "gray68", + "gray69", + "gray70", + "gray71", + "gray72", + "gray73", + "gray74", + "gray75", + "gray76", + "gray77", + "gray78", + "gray79", + "gray80", + "gray81", + "gray82", + "gray83", + "gray84", + "gray85", + "gray86", + "gray87", + "gray88", + "gray89", + "gray90", + "gray91", + "gray92", + "gray93", + "gray94", + "gray95", + "gray96", + "gray97", + "gray98", + "gray99", + "gray100", + "green", + "green1", + "green2", + "green3", + "green4", + "greenyellow", + "grey", + "grey0", + "grey1", + "grey2", + "grey3", + "grey4", + "grey5", + "grey6", + "grey7", + "grey8", + "grey9", + "grey10", + "grey11", + "grey12", + "grey13", + "grey14", + "grey15", + "grey16", + "grey17", + "grey18", + "grey19", + "grey20", + "grey21", + "grey22", + "grey23", + "grey24", + "grey25", + "grey26", + "grey27", + "grey28", + "grey29", + "grey30", + "grey31", + "grey32", + "grey33", + "grey34", + "grey35", + "grey36", + "grey37", + "grey38", + "grey39", + "grey40", + "grey41", + "grey42", + "grey43", + "grey44", + "grey45", + "grey46", + "grey47", + "grey48", + "grey49", + "grey50", + "grey51", + "grey52", + "grey53", + "grey54", + "grey55", + "grey56", + "grey57", + "grey58", + "grey59", + "grey60", + "grey61", + "grey62", + "grey63", + "grey64", + "grey65", + "grey66", + "grey67", + "grey68", + "grey69", + "grey70", + "grey71", + "grey72", + "grey73", + "grey74", + "grey75", + "grey76", + "grey77", + "grey78", + "grey79", + "grey80", + "grey81", + "grey82", + "grey83", + "grey84", + "grey85", + "grey86", + "grey87", + "grey88", + "grey89", + "grey90", + "grey91", + "grey92", + "grey93", + "grey94", + "grey95", + "grey96", + "grey97", + "grey98", + "grey99", + "grey100", + "honeydew", + "honeydew1", + "honeydew2", + "honeydew3", + "honeydew4", + "hotpink", + "hotpink1", + "hotpink2", + "hotpink3", + "hotpink4", + "indianred", + "indianred1", + "indianred2", + "indianred3", + "indianred4", + "ivory", + "ivory1", + "ivory2", + "ivory3", + "ivory4", + "khaki", + "khaki1", + "khaki2", + "khaki3", + "khaki4", + "lavender", + "lavenderblush", + "lavenderblush1", + "lavenderblush2", + "lavenderblush3", + "lavenderblush4", + "lawngreen", + "lemonchiffon", + "lemonchiffon1", + "lemonchiffon2", + "lemonchiffon3", + "lemonchiffon4", + "lightblue", + "lightblue1", + "lightblue2", + "lightblue3", + "lightblue4", + "lightcoral", + "lightcyan", + "lightcyan1", + "lightcyan2", + "lightcyan3", + "lightcyan4", + "lightgoldenrod", + "lightgoldenrod1", + "lightgoldenrod2", + "lightgoldenrod3", + "lightgoldenrod4", + "lightgoldenrodyellow", + "lightgray", + "lightgreen", + "lightgrey", + "lightpink", + "lightpink1", + "lightpink2", + "lightpink3", + "lightpink4", + "lightsalmon", + "lightsalmon1", + "lightsalmon2", + "lightsalmon3", + "lightsalmon4", + "lightseagreen", + "lightskyblue", + "lightskyblue1", + "lightskyblue2", + "lightskyblue3", + "lightskyblue4", + "lightslateblue", + "lightslategray", + "lightslategrey", + "lightsteelblue", + "lightsteelblue1", + "lightsteelblue2", + "lightsteelblue3", + "lightsteelblue4", + "lightyellow", + "lightyellow1", + "lightyellow2", + "lightyellow3", + "lightyellow4", + "limegreen", + "linen", + "magenta", + "magenta1", + "magenta2", + "magenta3", + "magenta4", + "maroon", + "maroon1", + "maroon2", + "maroon3", + "maroon4", + "mediumaquamarine", + "mediumblue", + "mediumorchid", + "mediumorchid1", + "mediumorchid2", + "mediumorchid3", + "mediumorchid4", + "mediumpurple", + "mediumpurple1", + "mediumpurple2", + "mediumpurple3", + "mediumpurple4", + "mediumseagreen", + "mediumslateblue", + "mediumspringgreen", + "mediumturquoise", + "mediumvioletred", + "midnightblue", + "mintcream", + "mistyrose", + "mistyrose1", + "mistyrose2", + "mistyrose3", + "mistyrose4", + "moccasin", + "navajowhite", + "navajowhite1", + "navajowhite2", + "navajowhite3", + "navajowhite4", + "navy", + "navyblue", + "oldlace", + "olivedrab", + "olivedrab1", + "olivedrab2", + "olivedrab3", + "olivedrab4", + "orange", + "orange1", + "orange2", + "orange3", + "orange4", + "orangered", + "orangered1", + "orangered2", + "orangered3", + "orangered4", + "orchid", + "orchid1", + "orchid2", + "orchid3", + "orchid4", + "palegoldenrod", + "palegreen", + "palegreen1", + "palegreen2", + "palegreen3", + "palegreen4", + "paleturquoise", + "paleturquoise1", + "paleturquoise2", + "paleturquoise3", + "paleturquoise4", + "palevioletred", + "palevioletred1", + "palevioletred2", + "palevioletred3", + "palevioletred4", + "papayawhip", + "peachpuff", + "peachpuff1", + "peachpuff2", + "peachpuff3", + "peachpuff4", + "peru", + "pink", + "pink1", + "pink2", + "pink3", + "pink4", + "plum", + "plum1", + "plum2", + "plum3", + "plum4", + "powderblue", + "purple", + "purple1", + "purple2", + "purple3", + "purple4", + "red", + "red1", + "red2", + "red3", + "red4", + "rosybrown", + "rosybrown1", + "rosybrown2", + "rosybrown3", + "rosybrown4", + "royalblue", + "royalblue1", + "royalblue2", + "royalblue3", + "royalblue4", + "saddlebrown", + "salmon", + "salmon1", + "salmon2", + "salmon3", + "salmon4", + "sandybrown", + "seagreen", + "seagreen1", + "seagreen2", + "seagreen3", + "seagreen4", + "seashell", + "seashell1", + "seashell2", + "seashell3", + "seashell4", + "sienna", + "sienna1", + "sienna2", + "sienna3", + "sienna4", + "skyblue", + "skyblue1", + "skyblue2", + "skyblue3", + "skyblue4", + "slateblue", + "slateblue1", + "slateblue2", + "slateblue3", + "slateblue4", + "slategray", + "slategray1", + "slategray2", + "slategray3", + "slategray4", + "slategrey", + "snow", + "snow1", + "snow2", + "snow3", + "snow4", + "springgreen", + "springgreen1", + "springgreen2", + "springgreen3", + "springgreen4", + "steelblue", + "steelblue1", + "steelblue2", + "steelblue3", + "steelblue4", + "tan", + "tan1", + "tan2", + "tan3", + "tan4", + "thistle", + "thistle1", + "thistle2", + "thistle3", + "thistle4", + "tomato", + "tomato1", + "tomato2", + "tomato3", + "tomato4", + "turquoise", + "turquoise1", + "turquoise2", + "turquoise3", + "turquoise4", + "violet", + "violetred", + "violetred1", + "violetred2", + "violetred3", + "violetred4", + "wheat", + "wheat1", + "wheat2", + "wheat3", + "wheat4", + "whitesmoke", + "yellow", + "yellow1", + "yellow2", + "yellow3", + "yellow4", + "yellowgreen" + ], + "defaultValue": "blue", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "color_of_non_significant_features", + "displayName": "Color of Non-Significant Features", + "description": "", + "paramType": "SELECT", + "paramGroup": "Plot", + "paramValues": [ + "white", + "aliceblue", + "antiquewhite", + "antiquewhite1", + "antiquewhite2", + "antiquewhite3", + "antiquewhite4", + "aquamarine", + "aquamarine1", + "aquamarine2", + "aquamarine3", + "aquamarine4", + "azure", + "azure1", + "azure2", + "azure3", + "azure4", + "beige", + "bisque", + "bisque1", + "bisque2", + "bisque3", + "bisque4", + "black", + "blanchedalmond", + "blue", + "blue1", + "blue2", + "blue3", + "blue4", + "blueviolet", + "brown", + "brown1", + "brown2", + "brown3", + "brown4", + "burlywood", + "burlywood1", + "burlywood2", + "burlywood3", + "burlywood4", + "cadetblue", + "cadetblue1", + "cadetblue2", + "cadetblue3", + "cadetblue4", + "chartreuse", + "chartreuse1", + "chartreuse2", + "chartreuse3", + "chartreuse4", + "chocolate", + "chocolate1", + "chocolate2", + "chocolate3", + "chocolate4", + "coral", + "coral1", + "coral2", + "coral3", + "coral4", + "cornflowerblue", + "cornsilk", + "cornsilk1", + "cornsilk2", + "cornsilk3", + "cornsilk4", + "cyan", + "cyan1", + "cyan2", + "cyan3", + "cyan4", + "darkblue", + "darkcyan", + "darkgoldenrod", + "darkgoldenrod1", + "darkgoldenrod2", + "darkgoldenrod3", + "darkgoldenrod4", + "darkgray", + "darkgreen", + "darkgrey", + "darkkhaki", + "darkmagenta", + "darkolivegreen", + "darkolivegreen1", + "darkolivegreen2", + "darkolivegreen3", + "darkolivegreen4", + "darkorange", + "darkorange1", + "darkorange2", + "darkorange3", + "darkorange4", + "darkorchid", + "darkorchid1", + "darkorchid2", + "darkorchid3", + "darkorchid4", + "darkred", + "darksalmon", + "darkseagreen", + "darkseagreen1", + "darkseagreen2", + "darkseagreen3", + "darkseagreen4", + "darkslateblue", + "darkslategray", + "darkslategray1", + "darkslategray2", + "darkslategray3", + "darkslategray4", + "darkslategrey", + "darkturquoise", + "darkviolet", + "deeppink", + "deeppink1", + "deeppink2", + "deeppink3", + "deeppink4", + "deepskyblue", + "deepskyblue1", + "deepskyblue2", + "deepskyblue3", + "deepskyblue4", + "dimgray", + "dimgrey", + "dodgerblue", + "dodgerblue1", + "dodgerblue2", + "dodgerblue3", + "dodgerblue4", + "firebrick", + "firebrick1", + "firebrick2", + "firebrick3", + "firebrick4", + "floralwhite", + "forestgreen", + "gainsboro", + "ghostwhite", + "gold", + "gold1", + "gold2", + "gold3", + "gold4", + "goldenrod", + "goldenrod1", + "goldenrod2", + "goldenrod3", + "goldenrod4", + "gray", + "gray0", + "gray1", + "gray2", + "gray3", + "gray4", + "gray5", + "gray6", + "gray7", + "gray8", + "gray9", + "gray10", + "gray11", + "gray12", + "gray13", + "gray14", + "gray15", + "gray16", + "gray17", + "gray18", + "gray19", + "gray20", + "gray21", + "gray22", + "gray23", + "gray24", + "gray25", + "gray26", + "gray27", + "gray28", + "gray29", + "gray30", + "gray31", + "gray32", + "gray33", + "gray34", + "gray35", + "gray36", + "gray37", + "gray38", + "gray39", + "gray40", + "gray41", + "gray42", + "gray43", + "gray44", + "gray45", + "gray46", + "gray47", + "gray48", + "gray49", + "gray50", + "gray51", + "gray52", + "gray53", + "gray54", + "gray55", + "gray56", + "gray57", + "gray58", + "gray59", + "gray60", + "gray61", + "gray62", + "gray63", + "gray64", + "gray65", + "gray66", + "gray67", + "gray68", + "gray69", + "gray70", + "gray71", + "gray72", + "gray73", + "gray74", + "gray75", + "gray76", + "gray77", + "gray78", + "gray79", + "gray80", + "gray81", + "gray82", + "gray83", + "gray84", + "gray85", + "gray86", + "gray87", + "gray88", + "gray89", + "gray90", + "gray91", + "gray92", + "gray93", + "gray94", + "gray95", + "gray96", + "gray97", + "gray98", + "gray99", + "gray100", + "green", + "green1", + "green2", + "green3", + "green4", + "greenyellow", + "grey", + "grey0", + "grey1", + "grey2", + "grey3", + "grey4", + "grey5", + "grey6", + "grey7", + "grey8", + "grey9", + "grey10", + "grey11", + "grey12", + "grey13", + "grey14", + "grey15", + "grey16", + "grey17", + "grey18", + "grey19", + "grey20", + "grey21", + "grey22", + "grey23", + "grey24", + "grey25", + "grey26", + "grey27", + "grey28", + "grey29", + "grey30", + "grey31", + "grey32", + "grey33", + "grey34", + "grey35", + "grey36", + "grey37", + "grey38", + "grey39", + "grey40", + "grey41", + "grey42", + "grey43", + "grey44", + "grey45", + "grey46", + "grey47", + "grey48", + "grey49", + "grey50", + "grey51", + "grey52", + "grey53", + "grey54", + "grey55", + "grey56", + "grey57", + "grey58", + "grey59", + "grey60", + "grey61", + "grey62", + "grey63", + "grey64", + "grey65", + "grey66", + "grey67", + "grey68", + "grey69", + "grey70", + "grey71", + "grey72", + "grey73", + "grey74", + "grey75", + "grey76", + "grey77", + "grey78", + "grey79", + "grey80", + "grey81", + "grey82", + "grey83", + "grey84", + "grey85", + "grey86", + "grey87", + "grey88", + "grey89", + "grey90", + "grey91", + "grey92", + "grey93", + "grey94", + "grey95", + "grey96", + "grey97", + "grey98", + "grey99", + "grey100", + "honeydew", + "honeydew1", + "honeydew2", + "honeydew3", + "honeydew4", + "hotpink", + "hotpink1", + "hotpink2", + "hotpink3", + "hotpink4", + "indianred", + "indianred1", + "indianred2", + "indianred3", + "indianred4", + "ivory", + "ivory1", + "ivory2", + "ivory3", + "ivory4", + "khaki", + "khaki1", + "khaki2", + "khaki3", + "khaki4", + "lavender", + "lavenderblush", + "lavenderblush1", + "lavenderblush2", + "lavenderblush3", + "lavenderblush4", + "lawngreen", + "lemonchiffon", + "lemonchiffon1", + "lemonchiffon2", + "lemonchiffon3", + "lemonchiffon4", + "lightblue", + "lightblue1", + "lightblue2", + "lightblue3", + "lightblue4", + "lightcoral", + "lightcyan", + "lightcyan1", + "lightcyan2", + "lightcyan3", + "lightcyan4", + "lightgoldenrod", + "lightgoldenrod1", + "lightgoldenrod2", + "lightgoldenrod3", + "lightgoldenrod4", + "lightgoldenrodyellow", + "lightgray", + "lightgreen", + "lightgrey", + "lightpink", + "lightpink1", + "lightpink2", + "lightpink3", + "lightpink4", + "lightsalmon", + "lightsalmon1", + "lightsalmon2", + "lightsalmon3", + "lightsalmon4", + "lightseagreen", + "lightskyblue", + "lightskyblue1", + "lightskyblue2", + "lightskyblue3", + "lightskyblue4", + "lightslateblue", + "lightslategray", + "lightslategrey", + "lightsteelblue", + "lightsteelblue1", + "lightsteelblue2", + "lightsteelblue3", + "lightsteelblue4", + "lightyellow", + "lightyellow1", + "lightyellow2", + "lightyellow3", + "lightyellow4", + "limegreen", + "linen", + "magenta", + "magenta1", + "magenta2", + "magenta3", + "magenta4", + "maroon", + "maroon1", + "maroon2", + "maroon3", + "maroon4", + "mediumaquamarine", + "mediumblue", + "mediumorchid", + "mediumorchid1", + "mediumorchid2", + "mediumorchid3", + "mediumorchid4", + "mediumpurple", + "mediumpurple1", + "mediumpurple2", + "mediumpurple3", + "mediumpurple4", + "mediumseagreen", + "mediumslateblue", + "mediumspringgreen", + "mediumturquoise", + "mediumvioletred", + "midnightblue", + "mintcream", + "mistyrose", + "mistyrose1", + "mistyrose2", + "mistyrose3", + "mistyrose4", + "moccasin", + "navajowhite", + "navajowhite1", + "navajowhite2", + "navajowhite3", + "navajowhite4", + "navy", + "navyblue", + "oldlace", + "olivedrab", + "olivedrab1", + "olivedrab2", + "olivedrab3", + "olivedrab4", + "orange", + "orange1", + "orange2", + "orange3", + "orange4", + "orangered", + "orangered1", + "orangered2", + "orangered3", + "orangered4", + "orchid", + "orchid1", + "orchid2", + "orchid3", + "orchid4", + "palegoldenrod", + "palegreen", + "palegreen1", + "palegreen2", + "palegreen3", + "palegreen4", + "paleturquoise", + "paleturquoise1", + "paleturquoise2", + "paleturquoise3", + "paleturquoise4", + "palevioletred", + "palevioletred1", + "palevioletred2", + "palevioletred3", + "palevioletred4", + "papayawhip", + "peachpuff", + "peachpuff1", + "peachpuff2", + "peachpuff3", + "peachpuff4", + "peru", + "pink", + "pink1", + "pink2", + "pink3", + "pink4", + "plum", + "plum1", + "plum2", + "plum3", + "plum4", + "powderblue", + "purple", + "purple1", + "purple2", + "purple3", + "purple4", + "red", + "red1", + "red2", + "red3", + "red4", + "rosybrown", + "rosybrown1", + "rosybrown2", + "rosybrown3", + "rosybrown4", + "royalblue", + "royalblue1", + "royalblue2", + "royalblue3", + "royalblue4", + "saddlebrown", + "salmon", + "salmon1", + "salmon2", + "salmon3", + "salmon4", + "sandybrown", + "seagreen", + "seagreen1", + "seagreen2", + "seagreen3", + "seagreen4", + "seashell", + "seashell1", + "seashell2", + "seashell3", + "seashell4", + "sienna", + "sienna1", + "sienna2", + "sienna3", + "sienna4", + "skyblue", + "skyblue1", + "skyblue2", + "skyblue3", + "skyblue4", + "slateblue", + "slateblue1", + "slateblue2", + "slateblue3", + "slateblue4", + "slategray", + "slategray1", + "slategray2", + "slategray3", + "slategray4", + "slategrey", + "snow", + "snow1", + "snow2", + "snow3", + "snow4", + "springgreen", + "springgreen1", + "springgreen2", + "springgreen3", + "springgreen4", + "steelblue", + "steelblue1", + "steelblue2", + "steelblue3", + "steelblue4", + "tan", + "tan1", + "tan2", + "tan3", + "tan4", + "thistle", + "thistle1", + "thistle2", + "thistle3", + "thistle4", + "tomato", + "tomato1", + "tomato2", + "tomato3", + "tomato4", + "turquoise", + "turquoise1", + "turquoise2", + "turquoise3", + "turquoise4", + "violet", + "violetred", + "violetred1", + "violetred2", + "violetred3", + "violetred4", + "wheat", + "wheat1", + "wheat2", + "wheat3", + "wheat4", + "whitesmoke", + "yellow", + "yellow1", + "yellow2", + "yellow3", + "yellow4", + "yellowgreen" + ], + "defaultValue": "black", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "color_of_logfold_change_threshold_line", + "displayName": "Color of Log Fold Change Threshold Line", + "description": "The color of the vertical fold-change threshold lines", + "paramType": "SELECT", + "paramGroup": "Plot", + "paramValues": [ + "white", + "aliceblue", + "antiquewhite", + "antiquewhite1", + "antiquewhite2", + "antiquewhite3", + "antiquewhite4", + "aquamarine", + "aquamarine1", + "aquamarine2", + "aquamarine3", + "aquamarine4", + "azure", + "azure1", + "azure2", + "azure3", + "azure4", + "beige", + "bisque", + "bisque1", + "bisque2", + "bisque3", + "bisque4", + "black", + "blanchedalmond", + "blue", + "blue1", + "blue2", + "blue3", + "blue4", + "blueviolet", + "brown", + "brown1", + "brown2", + "brown3", + "brown4", + "burlywood", + "burlywood1", + "burlywood2", + "burlywood3", + "burlywood4", + "cadetblue", + "cadetblue1", + "cadetblue2", + "cadetblue3", + "cadetblue4", + "chartreuse", + "chartreuse1", + "chartreuse2", + "chartreuse3", + "chartreuse4", + "chocolate", + "chocolate1", + "chocolate2", + "chocolate3", + "chocolate4", + "coral", + "coral1", + "coral2", + "coral3", + "coral4", + "cornflowerblue", + "cornsilk", + "cornsilk1", + "cornsilk2", + "cornsilk3", + "cornsilk4", + "cyan", + "cyan1", + "cyan2", + "cyan3", + "cyan4", + "darkblue", + "darkcyan", + "darkgoldenrod", + "darkgoldenrod1", + "darkgoldenrod2", + "darkgoldenrod3", + "darkgoldenrod4", + "darkgray", + "darkgreen", + "darkgrey", + "darkkhaki", + "darkmagenta", + "darkolivegreen", + "darkolivegreen1", + "darkolivegreen2", + "darkolivegreen3", + "darkolivegreen4", + "darkorange", + "darkorange1", + "darkorange2", + "darkorange3", + "darkorange4", + "darkorchid", + "darkorchid1", + "darkorchid2", + "darkorchid3", + "darkorchid4", + "darkred", + "darksalmon", + "darkseagreen", + "darkseagreen1", + "darkseagreen2", + "darkseagreen3", + "darkseagreen4", + "darkslateblue", + "darkslategray", + "darkslategray1", + "darkslategray2", + "darkslategray3", + "darkslategray4", + "darkslategrey", + "darkturquoise", + "darkviolet", + "deeppink", + "deeppink1", + "deeppink2", + "deeppink3", + "deeppink4", + "deepskyblue", + "deepskyblue1", + "deepskyblue2", + "deepskyblue3", + "deepskyblue4", + "dimgray", + "dimgrey", + "dodgerblue", + "dodgerblue1", + "dodgerblue2", + "dodgerblue3", + "dodgerblue4", + "firebrick", + "firebrick1", + "firebrick2", + "firebrick3", + "firebrick4", + "floralwhite", + "forestgreen", + "gainsboro", + "ghostwhite", + "gold", + "gold1", + "gold2", + "gold3", + "gold4", + "goldenrod", + "goldenrod1", + "goldenrod2", + "goldenrod3", + "goldenrod4", + "gray", + "gray0", + "gray1", + "gray2", + "gray3", + "gray4", + "gray5", + "gray6", + "gray7", + "gray8", + "gray9", + "gray10", + "gray11", + "gray12", + "gray13", + "gray14", + "gray15", + "gray16", + "gray17", + "gray18", + "gray19", + "gray20", + "gray21", + "gray22", + "gray23", + "gray24", + "gray25", + "gray26", + "gray27", + "gray28", + "gray29", + "gray30", + "gray31", + "gray32", + "gray33", + "gray34", + "gray35", + "gray36", + "gray37", + "gray38", + "gray39", + "gray40", + "gray41", + "gray42", + "gray43", + "gray44", + "gray45", + "gray46", + "gray47", + "gray48", + "gray49", + "gray50", + "gray51", + "gray52", + "gray53", + "gray54", + "gray55", + "gray56", + "gray57", + "gray58", + "gray59", + "gray60", + "gray61", + "gray62", + "gray63", + "gray64", + "gray65", + "gray66", + "gray67", + "gray68", + "gray69", + "gray70", + "gray71", + "gray72", + "gray73", + "gray74", + "gray75", + "gray76", + "gray77", + "gray78", + "gray79", + "gray80", + "gray81", + "gray82", + "gray83", + "gray84", + "gray85", + "gray86", + "gray87", + "gray88", + "gray89", + "gray90", + "gray91", + "gray92", + "gray93", + "gray94", + "gray95", + "gray96", + "gray97", + "gray98", + "gray99", + "gray100", + "green", + "green1", + "green2", + "green3", + "green4", + "greenyellow", + "grey", + "grey0", + "grey1", + "grey2", + "grey3", + "grey4", + "grey5", + "grey6", + "grey7", + "grey8", + "grey9", + "grey10", + "grey11", + "grey12", + "grey13", + "grey14", + "grey15", + "grey16", + "grey17", + "grey18", + "grey19", + "grey20", + "grey21", + "grey22", + "grey23", + "grey24", + "grey25", + "grey26", + "grey27", + "grey28", + "grey29", + "grey30", + "grey31", + "grey32", + "grey33", + "grey34", + "grey35", + "grey36", + "grey37", + "grey38", + "grey39", + "grey40", + "grey41", + "grey42", + "grey43", + "grey44", + "grey45", + "grey46", + "grey47", + "grey48", + "grey49", + "grey50", + "grey51", + "grey52", + "grey53", + "grey54", + "grey55", + "grey56", + "grey57", + "grey58", + "grey59", + "grey60", + "grey61", + "grey62", + "grey63", + "grey64", + "grey65", + "grey66", + "grey67", + "grey68", + "grey69", + "grey70", + "grey71", + "grey72", + "grey73", + "grey74", + "grey75", + "grey76", + "grey77", + "grey78", + "grey79", + "grey80", + "grey81", + "grey82", + "grey83", + "grey84", + "grey85", + "grey86", + "grey87", + "grey88", + "grey89", + "grey90", + "grey91", + "grey92", + "grey93", + "grey94", + "grey95", + "grey96", + "grey97", + "grey98", + "grey99", + "grey100", + "honeydew", + "honeydew1", + "honeydew2", + "honeydew3", + "honeydew4", + "hotpink", + "hotpink1", + "hotpink2", + "hotpink3", + "hotpink4", + "indianred", + "indianred1", + "indianred2", + "indianred3", + "indianred4", + "ivory", + "ivory1", + "ivory2", + "ivory3", + "ivory4", + "khaki", + "khaki1", + "khaki2", + "khaki3", + "khaki4", + "lavender", + "lavenderblush", + "lavenderblush1", + "lavenderblush2", + "lavenderblush3", + "lavenderblush4", + "lawngreen", + "lemonchiffon", + "lemonchiffon1", + "lemonchiffon2", + "lemonchiffon3", + "lemonchiffon4", + "lightblue", + "lightblue1", + "lightblue2", + "lightblue3", + "lightblue4", + "lightcoral", + "lightcyan", + "lightcyan1", + "lightcyan2", + "lightcyan3", + "lightcyan4", + "lightgoldenrod", + "lightgoldenrod1", + "lightgoldenrod2", + "lightgoldenrod3", + "lightgoldenrod4", + "lightgoldenrodyellow", + "lightgray", + "lightgreen", + "lightgrey", + "lightpink", + "lightpink1", + "lightpink2", + "lightpink3", + "lightpink4", + "lightsalmon", + "lightsalmon1", + "lightsalmon2", + "lightsalmon3", + "lightsalmon4", + "lightseagreen", + "lightskyblue", + "lightskyblue1", + "lightskyblue2", + "lightskyblue3", + "lightskyblue4", + "lightslateblue", + "lightslategray", + "lightslategrey", + "lightsteelblue", + "lightsteelblue1", + "lightsteelblue2", + "lightsteelblue3", + "lightsteelblue4", + "lightyellow", + "lightyellow1", + "lightyellow2", + "lightyellow3", + "lightyellow4", + "limegreen", + "linen", + "magenta", + "magenta1", + "magenta2", + "magenta3", + "magenta4", + "maroon", + "maroon1", + "maroon2", + "maroon3", + "maroon4", + "mediumaquamarine", + "mediumblue", + "mediumorchid", + "mediumorchid1", + "mediumorchid2", + "mediumorchid3", + "mediumorchid4", + "mediumpurple", + "mediumpurple1", + "mediumpurple2", + "mediumpurple3", + "mediumpurple4", + "mediumseagreen", + "mediumslateblue", + "mediumspringgreen", + "mediumturquoise", + "mediumvioletred", + "midnightblue", + "mintcream", + "mistyrose", + "mistyrose1", + "mistyrose2", + "mistyrose3", + "mistyrose4", + "moccasin", + "navajowhite", + "navajowhite1", + "navajowhite2", + "navajowhite3", + "navajowhite4", + "navy", + "navyblue", + "oldlace", + "olivedrab", + "olivedrab1", + "olivedrab2", + "olivedrab3", + "olivedrab4", + "orange", + "orange1", + "orange2", + "orange3", + "orange4", + "orangered", + "orangered1", + "orangered2", + "orangered3", + "orangered4", + "orchid", + "orchid1", + "orchid2", + "orchid3", + "orchid4", + "palegoldenrod", + "palegreen", + "palegreen1", + "palegreen2", + "palegreen3", + "palegreen4", + "paleturquoise", + "paleturquoise1", + "paleturquoise2", + "paleturquoise3", + "paleturquoise4", + "palevioletred", + "palevioletred1", + "palevioletred2", + "palevioletred3", + "palevioletred4", + "papayawhip", + "peachpuff", + "peachpuff1", + "peachpuff2", + "peachpuff3", + "peachpuff4", + "peru", + "pink", + "pink1", + "pink2", + "pink3", + "pink4", + "plum", + "plum1", + "plum2", + "plum3", + "plum4", + "powderblue", + "purple", + "purple1", + "purple2", + "purple3", + "purple4", + "red", + "red1", + "red2", + "red3", + "red4", + "rosybrown", + "rosybrown1", + "rosybrown2", + "rosybrown3", + "rosybrown4", + "royalblue", + "royalblue1", + "royalblue2", + "royalblue3", + "royalblue4", + "saddlebrown", + "salmon", + "salmon1", + "salmon2", + "salmon3", + "salmon4", + "sandybrown", + "seagreen", + "seagreen1", + "seagreen2", + "seagreen3", + "seagreen4", + "seashell", + "seashell1", + "seashell2", + "seashell3", + "seashell4", + "sienna", + "sienna1", + "sienna2", + "sienna3", + "sienna4", + "skyblue", + "skyblue1", + "skyblue2", + "skyblue3", + "skyblue4", + "slateblue", + "slateblue1", + "slateblue2", + "slateblue3", + "slateblue4", + "slategray", + "slategray1", + "slategray2", + "slategray3", + "slategray4", + "slategrey", + "snow", + "snow1", + "snow2", + "snow3", + "snow4", + "springgreen", + "springgreen1", + "springgreen2", + "springgreen3", + "springgreen4", + "steelblue", + "steelblue1", + "steelblue2", + "steelblue3", + "steelblue4", + "tan", + "tan1", + "tan2", + "tan3", + "tan4", + "thistle", + "thistle1", + "thistle2", + "thistle3", + "thistle4", + "tomato", + "tomato1", + "tomato2", + "tomato3", + "tomato4", + "turquoise", + "turquoise1", + "turquoise2", + "turquoise3", + "turquoise4", + "violet", + "violetred", + "violetred1", + "violetred2", + "violetred3", + "violetred4", + "wheat", + "wheat1", + "wheat2", + "wheat3", + "wheat4", + "whitesmoke", + "yellow", + "yellow1", + "yellow2", + "yellow3", + "yellow4", + "yellowgreen" + ], + "defaultValue": "red", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "color_of_features_meeting_only_signif_threshold", + "displayName": "Color of Features Meeting Only P-Value Threshold", + "description": "", + "paramType": "SELECT", + "paramGroup": "Plot", + "paramValues": [ + "white", + "aliceblue", + "antiquewhite", + "antiquewhite1", + "antiquewhite2", + "antiquewhite3", + "antiquewhite4", + "aquamarine", + "aquamarine1", + "aquamarine2", + "aquamarine3", + "aquamarine4", + "azure", + "azure1", + "azure2", + "azure3", + "azure4", + "beige", + "bisque", + "bisque1", + "bisque2", + "bisque3", + "bisque4", + "black", + "blanchedalmond", + "blue", + "blue1", + "blue2", + "blue3", + "blue4", + "blueviolet", + "brown", + "brown1", + "brown2", + "brown3", + "brown4", + "burlywood", + "burlywood1", + "burlywood2", + "burlywood3", + "burlywood4", + "cadetblue", + "cadetblue1", + "cadetblue2", + "cadetblue3", + "cadetblue4", + "chartreuse", + "chartreuse1", + "chartreuse2", + "chartreuse3", + "chartreuse4", + "chocolate", + "chocolate1", + "chocolate2", + "chocolate3", + "chocolate4", + "coral", + "coral1", + "coral2", + "coral3", + "coral4", + "cornflowerblue", + "cornsilk", + "cornsilk1", + "cornsilk2", + "cornsilk3", + "cornsilk4", + "cyan", + "cyan1", + "cyan2", + "cyan3", + "cyan4", + "darkblue", + "darkcyan", + "darkgoldenrod", + "darkgoldenrod1", + "darkgoldenrod2", + "darkgoldenrod3", + "darkgoldenrod4", + "darkgray", + "darkgreen", + "darkgrey", + "darkkhaki", + "darkmagenta", + "darkolivegreen", + "darkolivegreen1", + "darkolivegreen2", + "darkolivegreen3", + "darkolivegreen4", + "darkorange", + "darkorange1", + "darkorange2", + "darkorange3", + "darkorange4", + "darkorchid", + "darkorchid1", + "darkorchid2", + "darkorchid3", + "darkorchid4", + "darkred", + "darksalmon", + "darkseagreen", + "darkseagreen1", + "darkseagreen2", + "darkseagreen3", + "darkseagreen4", + "darkslateblue", + "darkslategray", + "darkslategray1", + "darkslategray2", + "darkslategray3", + "darkslategray4", + "darkslategrey", + "darkturquoise", + "darkviolet", + "deeppink", + "deeppink1", + "deeppink2", + "deeppink3", + "deeppink4", + "deepskyblue", + "deepskyblue1", + "deepskyblue2", + "deepskyblue3", + "deepskyblue4", + "dimgray", + "dimgrey", + "dodgerblue", + "dodgerblue1", + "dodgerblue2", + "dodgerblue3", + "dodgerblue4", + "firebrick", + "firebrick1", + "firebrick2", + "firebrick3", + "firebrick4", + "floralwhite", + "forestgreen", + "gainsboro", + "ghostwhite", + "gold", + "gold1", + "gold2", + "gold3", + "gold4", + "goldenrod", + "goldenrod1", + "goldenrod2", + "goldenrod3", + "goldenrod4", + "gray", + "gray0", + "gray1", + "gray2", + "gray3", + "gray4", + "gray5", + "gray6", + "gray7", + "gray8", + "gray9", + "gray10", + "gray11", + "gray12", + "gray13", + "gray14", + "gray15", + "gray16", + "gray17", + "gray18", + "gray19", + "gray20", + "gray21", + "gray22", + "gray23", + "gray24", + "gray25", + "gray26", + "gray27", + "gray28", + "gray29", + "gray30", + "gray31", + "gray32", + "gray33", + "gray34", + "gray35", + "gray36", + "gray37", + "gray38", + "gray39", + "gray40", + "gray41", + "gray42", + "gray43", + "gray44", + "gray45", + "gray46", + "gray47", + "gray48", + "gray49", + "gray50", + "gray51", + "gray52", + "gray53", + "gray54", + "gray55", + "gray56", + "gray57", + "gray58", + "gray59", + "gray60", + "gray61", + "gray62", + "gray63", + "gray64", + "gray65", + "gray66", + "gray67", + "gray68", + "gray69", + "gray70", + "gray71", + "gray72", + "gray73", + "gray74", + "gray75", + "gray76", + "gray77", + "gray78", + "gray79", + "gray80", + "gray81", + "gray82", + "gray83", + "gray84", + "gray85", + "gray86", + "gray87", + "gray88", + "gray89", + "gray90", + "gray91", + "gray92", + "gray93", + "gray94", + "gray95", + "gray96", + "gray97", + "gray98", + "gray99", + "gray100", + "green", + "green1", + "green2", + "green3", + "green4", + "greenyellow", + "grey", + "grey0", + "grey1", + "grey2", + "grey3", + "grey4", + "grey5", + "grey6", + "grey7", + "grey8", + "grey9", + "grey10", + "grey11", + "grey12", + "grey13", + "grey14", + "grey15", + "grey16", + "grey17", + "grey18", + "grey19", + "grey20", + "grey21", + "grey22", + "grey23", + "grey24", + "grey25", + "grey26", + "grey27", + "grey28", + "grey29", + "grey30", + "grey31", + "grey32", + "grey33", + "grey34", + "grey35", + "grey36", + "grey37", + "grey38", + "grey39", + "grey40", + "grey41", + "grey42", + "grey43", + "grey44", + "grey45", + "grey46", + "grey47", + "grey48", + "grey49", + "grey50", + "grey51", + "grey52", + "grey53", + "grey54", + "grey55", + "grey56", + "grey57", + "grey58", + "grey59", + "grey60", + "grey61", + "grey62", + "grey63", + "grey64", + "grey65", + "grey66", + "grey67", + "grey68", + "grey69", + "grey70", + "grey71", + "grey72", + "grey73", + "grey74", + "grey75", + "grey76", + "grey77", + "grey78", + "grey79", + "grey80", + "grey81", + "grey82", + "grey83", + "grey84", + "grey85", + "grey86", + "grey87", + "grey88", + "grey89", + "grey90", + "grey91", + "grey92", + "grey93", + "grey94", + "grey95", + "grey96", + "grey97", + "grey98", + "grey99", + "grey100", + "honeydew", + "honeydew1", + "honeydew2", + "honeydew3", + "honeydew4", + "hotpink", + "hotpink1", + "hotpink2", + "hotpink3", + "hotpink4", + "indianred", + "indianred1", + "indianred2", + "indianred3", + "indianred4", + "ivory", + "ivory1", + "ivory2", + "ivory3", + "ivory4", + "khaki", + "khaki1", + "khaki2", + "khaki3", + "khaki4", + "lavender", + "lavenderblush", + "lavenderblush1", + "lavenderblush2", + "lavenderblush3", + "lavenderblush4", + "lawngreen", + "lemonchiffon", + "lemonchiffon1", + "lemonchiffon2", + "lemonchiffon3", + "lemonchiffon4", + "lightblue", + "lightblue1", + "lightblue2", + "lightblue3", + "lightblue4", + "lightcoral", + "lightcyan", + "lightcyan1", + "lightcyan2", + "lightcyan3", + "lightcyan4", + "lightgoldenrod", + "lightgoldenrod1", + "lightgoldenrod2", + "lightgoldenrod3", + "lightgoldenrod4", + "lightgoldenrodyellow", + "lightgray", + "lightgreen", + "lightgrey", + "lightpink", + "lightpink1", + "lightpink2", + "lightpink3", + "lightpink4", + "lightsalmon", + "lightsalmon1", + "lightsalmon2", + "lightsalmon3", + "lightsalmon4", + "lightseagreen", + "lightskyblue", + "lightskyblue1", + "lightskyblue2", + "lightskyblue3", + "lightskyblue4", + "lightslateblue", + "lightslategray", + "lightslategrey", + "lightsteelblue", + "lightsteelblue1", + "lightsteelblue2", + "lightsteelblue3", + "lightsteelblue4", + "lightyellow", + "lightyellow1", + "lightyellow2", + "lightyellow3", + "lightyellow4", + "limegreen", + "linen", + "magenta", + "magenta1", + "magenta2", + "magenta3", + "magenta4", + "maroon", + "maroon1", + "maroon2", + "maroon3", + "maroon4", + "mediumaquamarine", + "mediumblue", + "mediumorchid", + "mediumorchid1", + "mediumorchid2", + "mediumorchid3", + "mediumorchid4", + "mediumpurple", + "mediumpurple1", + "mediumpurple2", + "mediumpurple3", + "mediumpurple4", + "mediumseagreen", + "mediumslateblue", + "mediumspringgreen", + "mediumturquoise", + "mediumvioletred", + "midnightblue", + "mintcream", + "mistyrose", + "mistyrose1", + "mistyrose2", + "mistyrose3", + "mistyrose4", + "moccasin", + "navajowhite", + "navajowhite1", + "navajowhite2", + "navajowhite3", + "navajowhite4", + "navy", + "navyblue", + "oldlace", + "olivedrab", + "olivedrab1", + "olivedrab2", + "olivedrab3", + "olivedrab4", + "orange", + "orange1", + "orange2", + "orange3", + "orange4", + "orangered", + "orangered1", + "orangered2", + "orangered3", + "orangered4", + "orchid", + "orchid1", + "orchid2", + "orchid3", + "orchid4", + "palegoldenrod", + "palegreen", + "palegreen1", + "palegreen2", + "palegreen3", + "palegreen4", + "paleturquoise", + "paleturquoise1", + "paleturquoise2", + "paleturquoise3", + "paleturquoise4", + "palevioletred", + "palevioletred1", + "palevioletred2", + "palevioletred3", + "palevioletred4", + "papayawhip", + "peachpuff", + "peachpuff1", + "peachpuff2", + "peachpuff3", + "peachpuff4", + "peru", + "pink", + "pink1", + "pink2", + "pink3", + "pink4", + "plum", + "plum1", + "plum2", + "plum3", + "plum4", + "powderblue", + "purple", + "purple1", + "purple2", + "purple3", + "purple4", + "red", + "red1", + "red2", + "red3", + "red4", + "rosybrown", + "rosybrown1", + "rosybrown2", + "rosybrown3", + "rosybrown4", + "royalblue", + "royalblue1", + "royalblue2", + "royalblue3", + "royalblue4", + "saddlebrown", + "salmon", + "salmon1", + "salmon2", + "salmon3", + "salmon4", + "sandybrown", + "seagreen", + "seagreen1", + "seagreen2", + "seagreen3", + "seagreen4", + "seashell", + "seashell1", + "seashell2", + "seashell3", + "seashell4", + "sienna", + "sienna1", + "sienna2", + "sienna3", + "sienna4", + "skyblue", + "skyblue1", + "skyblue2", + "skyblue3", + "skyblue4", + "slateblue", + "slateblue1", + "slateblue2", + "slateblue3", + "slateblue4", + "slategray", + "slategray1", + "slategray2", + "slategray3", + "slategray4", + "slategrey", + "snow", + "snow1", + "snow2", + "snow3", + "snow4", + "springgreen", + "springgreen1", + "springgreen2", + "springgreen3", + "springgreen4", + "steelblue", + "steelblue1", + "steelblue2", + "steelblue3", + "steelblue4", + "tan", + "tan1", + "tan2", + "tan3", + "tan4", + "thistle", + "thistle1", + "thistle2", + "thistle3", + "thistle4", + "tomato", + "tomato1", + "tomato2", + "tomato3", + "tomato4", + "turquoise", + "turquoise1", + "turquoise2", + "turquoise3", + "turquoise4", + "violet", + "violetred", + "violetred1", + "violetred2", + "violetred3", + "violetred4", + "wheat", + "wheat1", + "wheat2", + "wheat3", + "wheat4", + "whitesmoke", + "yellow", + "yellow1", + "yellow2", + "yellow3", + "yellow4", + "yellowgreen" + ], + "defaultValue": "lightgoldenrod2", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "color_for_features_meeting_pvalue_and_foldchange_thresholds", + "displayName": "Color for features meeting p-value and fold-change thresholds", + "description": "", + "paramType": "SELECT", + "paramGroup": "Plot", + "paramValues": [ + "white", + "aliceblue", + "antiquewhite", + "antiquewhite1", + "antiquewhite2", + "antiquewhite3", + "antiquewhite4", + "aquamarine", + "aquamarine1", + "aquamarine2", + "aquamarine3", + "aquamarine4", + "azure", + "azure1", + "azure2", + "azure3", + "azure4", + "beige", + "bisque", + "bisque1", + "bisque2", + "bisque3", + "bisque4", + "black", + "blanchedalmond", + "blue", + "blue1", + "blue2", + "blue3", + "blue4", + "blueviolet", + "brown", + "brown1", + "brown2", + "brown3", + "brown4", + "burlywood", + "burlywood1", + "burlywood2", + "burlywood3", + "burlywood4", + "cadetblue", + "cadetblue1", + "cadetblue2", + "cadetblue3", + "cadetblue4", + "chartreuse", + "chartreuse1", + "chartreuse2", + "chartreuse3", + "chartreuse4", + "chocolate", + "chocolate1", + "chocolate2", + "chocolate3", + "chocolate4", + "coral", + "coral1", + "coral2", + "coral3", + "coral4", + "cornflowerblue", + "cornsilk", + "cornsilk1", + "cornsilk2", + "cornsilk3", + "cornsilk4", + "cyan", + "cyan1", + "cyan2", + "cyan3", + "cyan4", + "darkblue", + "darkcyan", + "darkgoldenrod", + "darkgoldenrod1", + "darkgoldenrod2", + "darkgoldenrod3", + "darkgoldenrod4", + "darkgray", + "darkgreen", + "darkgrey", + "darkkhaki", + "darkmagenta", + "darkolivegreen", + "darkolivegreen1", + "darkolivegreen2", + "darkolivegreen3", + "darkolivegreen4", + "darkorange", + "darkorange1", + "darkorange2", + "darkorange3", + "darkorange4", + "darkorchid", + "darkorchid1", + "darkorchid2", + "darkorchid3", + "darkorchid4", + "darkred", + "darksalmon", + "darkseagreen", + "darkseagreen1", + "darkseagreen2", + "darkseagreen3", + "darkseagreen4", + "darkslateblue", + "darkslategray", + "darkslategray1", + "darkslategray2", + "darkslategray3", + "darkslategray4", + "darkslategrey", + "darkturquoise", + "darkviolet", + "deeppink", + "deeppink1", + "deeppink2", + "deeppink3", + "deeppink4", + "deepskyblue", + "deepskyblue1", + "deepskyblue2", + "deepskyblue3", + "deepskyblue4", + "dimgray", + "dimgrey", + "dodgerblue", + "dodgerblue1", + "dodgerblue2", + "dodgerblue3", + "dodgerblue4", + "firebrick", + "firebrick1", + "firebrick2", + "firebrick3", + "firebrick4", + "floralwhite", + "forestgreen", + "gainsboro", + "ghostwhite", + "gold", + "gold1", + "gold2", + "gold3", + "gold4", + "goldenrod", + "goldenrod1", + "goldenrod2", + "goldenrod3", + "goldenrod4", + "gray", + "gray0", + "gray1", + "gray2", + "gray3", + "gray4", + "gray5", + "gray6", + "gray7", + "gray8", + "gray9", + "gray10", + "gray11", + "gray12", + "gray13", + "gray14", + "gray15", + "gray16", + "gray17", + "gray18", + "gray19", + "gray20", + "gray21", + "gray22", + "gray23", + "gray24", + "gray25", + "gray26", + "gray27", + "gray28", + "gray29", + "gray30", + "gray31", + "gray32", + "gray33", + "gray34", + "gray35", + "gray36", + "gray37", + "gray38", + "gray39", + "gray40", + "gray41", + "gray42", + "gray43", + "gray44", + "gray45", + "gray46", + "gray47", + "gray48", + "gray49", + "gray50", + "gray51", + "gray52", + "gray53", + "gray54", + "gray55", + "gray56", + "gray57", + "gray58", + "gray59", + "gray60", + "gray61", + "gray62", + "gray63", + "gray64", + "gray65", + "gray66", + "gray67", + "gray68", + "gray69", + "gray70", + "gray71", + "gray72", + "gray73", + "gray74", + "gray75", + "gray76", + "gray77", + "gray78", + "gray79", + "gray80", + "gray81", + "gray82", + "gray83", + "gray84", + "gray85", + "gray86", + "gray87", + "gray88", + "gray89", + "gray90", + "gray91", + "gray92", + "gray93", + "gray94", + "gray95", + "gray96", + "gray97", + "gray98", + "gray99", + "gray100", + "green", + "green1", + "green2", + "green3", + "green4", + "greenyellow", + "grey", + "grey0", + "grey1", + "grey2", + "grey3", + "grey4", + "grey5", + "grey6", + "grey7", + "grey8", + "grey9", + "grey10", + "grey11", + "grey12", + "grey13", + "grey14", + "grey15", + "grey16", + "grey17", + "grey18", + "grey19", + "grey20", + "grey21", + "grey22", + "grey23", + "grey24", + "grey25", + "grey26", + "grey27", + "grey28", + "grey29", + "grey30", + "grey31", + "grey32", + "grey33", + "grey34", + "grey35", + "grey36", + "grey37", + "grey38", + "grey39", + "grey40", + "grey41", + "grey42", + "grey43", + "grey44", + "grey45", + "grey46", + "grey47", + "grey48", + "grey49", + "grey50", + "grey51", + "grey52", + "grey53", + "grey54", + "grey55", + "grey56", + "grey57", + "grey58", + "grey59", + "grey60", + "grey61", + "grey62", + "grey63", + "grey64", + "grey65", + "grey66", + "grey67", + "grey68", + "grey69", + "grey70", + "grey71", + "grey72", + "grey73", + "grey74", + "grey75", + "grey76", + "grey77", + "grey78", + "grey79", + "grey80", + "grey81", + "grey82", + "grey83", + "grey84", + "grey85", + "grey86", + "grey87", + "grey88", + "grey89", + "grey90", + "grey91", + "grey92", + "grey93", + "grey94", + "grey95", + "grey96", + "grey97", + "grey98", + "grey99", + "grey100", + "honeydew", + "honeydew1", + "honeydew2", + "honeydew3", + "honeydew4", + "hotpink", + "hotpink1", + "hotpink2", + "hotpink3", + "hotpink4", + "indianred", + "indianred1", + "indianred2", + "indianred3", + "indianred4", + "ivory", + "ivory1", + "ivory2", + "ivory3", + "ivory4", + "khaki", + "khaki1", + "khaki2", + "khaki3", + "khaki4", + "lavender", + "lavenderblush", + "lavenderblush1", + "lavenderblush2", + "lavenderblush3", + "lavenderblush4", + "lawngreen", + "lemonchiffon", + "lemonchiffon1", + "lemonchiffon2", + "lemonchiffon3", + "lemonchiffon4", + "lightblue", + "lightblue1", + "lightblue2", + "lightblue3", + "lightblue4", + "lightcoral", + "lightcyan", + "lightcyan1", + "lightcyan2", + "lightcyan3", + "lightcyan4", + "lightgoldenrod", + "lightgoldenrod1", + "lightgoldenrod2", + "lightgoldenrod3", + "lightgoldenrod4", + "lightgoldenrodyellow", + "lightgray", + "lightgreen", + "lightgrey", + "lightpink", + "lightpink1", + "lightpink2", + "lightpink3", + "lightpink4", + "lightsalmon", + "lightsalmon1", + "lightsalmon2", + "lightsalmon3", + "lightsalmon4", + "lightseagreen", + "lightskyblue", + "lightskyblue1", + "lightskyblue2", + "lightskyblue3", + "lightskyblue4", + "lightslateblue", + "lightslategray", + "lightslategrey", + "lightsteelblue", + "lightsteelblue1", + "lightsteelblue2", + "lightsteelblue3", + "lightsteelblue4", + "lightyellow", + "lightyellow1", + "lightyellow2", + "lightyellow3", + "lightyellow4", + "limegreen", + "linen", + "magenta", + "magenta1", + "magenta2", + "magenta3", + "magenta4", + "maroon", + "maroon1", + "maroon2", + "maroon3", + "maroon4", + "mediumaquamarine", + "mediumblue", + "mediumorchid", + "mediumorchid1", + "mediumorchid2", + "mediumorchid3", + "mediumorchid4", + "mediumpurple", + "mediumpurple1", + "mediumpurple2", + "mediumpurple3", + "mediumpurple4", + "mediumseagreen", + "mediumslateblue", + "mediumspringgreen", + "mediumturquoise", + "mediumvioletred", + "midnightblue", + "mintcream", + "mistyrose", + "mistyrose1", + "mistyrose2", + "mistyrose3", + "mistyrose4", + "moccasin", + "navajowhite", + "navajowhite1", + "navajowhite2", + "navajowhite3", + "navajowhite4", + "navy", + "navyblue", + "oldlace", + "olivedrab", + "olivedrab1", + "olivedrab2", + "olivedrab3", + "olivedrab4", + "orange", + "orange1", + "orange2", + "orange3", + "orange4", + "orangered", + "orangered1", + "orangered2", + "orangered3", + "orangered4", + "orchid", + "orchid1", + "orchid2", + "orchid3", + "orchid4", + "palegoldenrod", + "palegreen", + "palegreen1", + "palegreen2", + "palegreen3", + "palegreen4", + "paleturquoise", + "paleturquoise1", + "paleturquoise2", + "paleturquoise3", + "paleturquoise4", + "palevioletred", + "palevioletred1", + "palevioletred2", + "palevioletred3", + "palevioletred4", + "papayawhip", + "peachpuff", + "peachpuff1", + "peachpuff2", + "peachpuff3", + "peachpuff4", + "peru", + "pink", + "pink1", + "pink2", + "pink3", + "pink4", + "plum", + "plum1", + "plum2", + "plum3", + "plum4", + "powderblue", + "purple", + "purple1", + "purple2", + "purple3", + "purple4", + "red", + "red1", + "red2", + "red3", + "red4", + "rosybrown", + "rosybrown1", + "rosybrown2", + "rosybrown3", + "rosybrown4", + "royalblue", + "royalblue1", + "royalblue2", + "royalblue3", + "royalblue4", + "saddlebrown", + "salmon", + "salmon1", + "salmon2", + "salmon3", + "salmon4", + "sandybrown", + "seagreen", + "seagreen1", + "seagreen2", + "seagreen3", + "seagreen4", + "seashell", + "seashell1", + "seashell2", + "seashell3", + "seashell4", + "sienna", + "sienna1", + "sienna2", + "sienna3", + "sienna4", + "skyblue", + "skyblue1", + "skyblue2", + "skyblue3", + "skyblue4", + "slateblue", + "slateblue1", + "slateblue2", + "slateblue3", + "slateblue4", + "slategray", + "slategray1", + "slategray2", + "slategray3", + "slategray4", + "slategrey", + "snow", + "snow1", + "snow2", + "snow3", + "snow4", + "springgreen", + "springgreen1", + "springgreen2", + "springgreen3", + "springgreen4", + "steelblue", + "steelblue1", + "steelblue2", + "steelblue3", + "steelblue4", + "tan", + "tan1", + "tan2", + "tan3", + "tan4", + "thistle", + "thistle1", + "thistle2", + "thistle3", + "thistle4", + "tomato", + "tomato1", + "tomato2", + "tomato3", + "tomato4", + "turquoise", + "turquoise1", + "turquoise2", + "turquoise3", + "turquoise4", + "violet", + "violetred", + "violetred1", + "violetred2", + "violetred3", + "violetred4", + "wheat", + "wheat1", + "wheat2", + "wheat3", + "wheat4", + "whitesmoke", + "yellow", + "yellow1", + "yellow2", + "yellow3", + "yellow4", + "yellowgreen" + ], + "defaultValue": "red", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "flip_vplot", + "displayName": "Flip Contrast", + "description": "Select TRUE if you want to flip the contrast to opposite direction (flip the plot around the y-axis).", + "paramType": "BOOLEAN", + "paramGroup": "Plot", + "paramValues": null, + "defaultValue": "FALSE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "use_default_x_axis_limit", + "displayName": "Use Default X-Axis Limit", + "description": "Use default x limit", + "paramType": "BOOLEAN", + "paramGroup": "Plot", + "paramValues": null, + "defaultValue": "TRUE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "x_axis_limit", + "displayName": "X-Axis Limit", + "description": "The limits of the x-axis (symmetric about 0)", + "paramType": "NUMBER", + "paramGroup": "Plot", + "paramValues": null, + "defaultValue": "5", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "use_default_y_axis_limit", + "displayName": "Use Default Y-Axis Limit", + "description": "Use Default Y limit", + "paramType": "BOOLEAN", + "paramGroup": "Plot", + "paramValues": null, + "defaultValue": "TRUE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "y_axis_limit", + "displayName": "Y-Axis Limit", + "description": "The upper limit of the y-axis", + "paramType": "NUMBER", + "paramGroup": "Plot", + "paramValues": null, + "defaultValue": 10, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "point_size", + "displayName": "Point Size", + "description": "Size of a each data point", + "paramType": "NUMBER", + "paramGroup": "Plot", + "paramValues": null, + "defaultValue": 2, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "add_deg_columns", + "displayName": "Add DEG Columns to Output Table", + "description": "Select columns from input DEG results to include in the output dataset. If \"none\" is selected, then the output will contain only columns for Gene and Contrast.", + "paramType": "MULTISELECT", + "paramGroup": "Table", + "paramValues": ["FC", "logFC", "tstat", "pval", "adjpval"], + "defaultValue": ["FC", "logFC", "tstat", "pval", "adjpval"], + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "image_width", + "displayName": "Image Width", + "description": "Image width in inches", + "paramType": "NUMBER", + "paramGroup": "Image", + "paramValues": null, + "defaultValue": "15", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "image_height", + "displayName": "Image Height", + "description": "Image height in inches", + "paramType": "NUMBER", + "paramGroup": "Image", + "paramValues": null, + "defaultValue": "15", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "dpi", + "displayName": "Image Resolution", + "description": "Image resolution in dpi (dots-per-inch) for png output", + "paramType": "NUMBER", + "paramGroup": "Image", + "paramValues": null, + "defaultValue": "300", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "use_default_grid_layout", + "displayName": "Use Default Grid Layout", + "description": "if TRUE, an optimal number of rows in the figure grid layout is attempted; if you want to change the layout set the number of rows in the 'Number of rows in grid layout' parameter below", + "paramType": "BOOLEAN", + "paramGroup": "Image", + "paramValues": null, + "defaultValue": "TRUE", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "number_of_rows_in_grid_layout", + "displayName": "Number of Rows in Grid Layout", + "description": "", + "paramType": "NUMBER", + "paramGroup": "Image", + "paramValues": null, + "defaultValue": "1", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "aspect_ratio", + "displayName": "Figure Aspect Ratio", + "description": "figure aspect ratio, expressed as y / x; if 0, the ratio is based on the image size", + "paramType": "NUMBER", + "paramGroup": "Image", + "paramValues": null, + "defaultValue": "0", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "save_plots", + "displayName": "Save Plots", + "description": "If this is `TRUE`, any plots generated during the analysis will be saved to disk.", + "paramType": "BOOLEAN", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "outputDatasetName": "Volcano Plot - Summary", + "outputs": { + "DataFrame": { + "type": "file", + "name": "summary_dataframe.rds" + }, + "figures": { + "type": "file", + "name": "figures/diff/volcano_summary.png" + } + } +} \ No newline at end of file diff --git a/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/write_multiOmicDataSet_properties.json b/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/write_multiOmicDataSet_properties.json new file mode 100644 index 0000000..d18be56 --- /dev/null +++ b/code/MOSuite/inst/extdata/galaxy/1_mosuite-templates/write_multiOmicDataSet_properties.json @@ -0,0 +1,53 @@ +{ + "title": "Write multiOmicDataSet Properties", + "description": "Export the contents of a multiOmicDataSet (sample metadata, feature annotation, counts, and analyses) to a directory of CSV/RDS files for downstream use or inspection.", + "r_function": "write_multiOmicDataSet_properties", + "columns": [], + "inputDatasets": [ + { + "key": "moo_input_rds", + "displayName": "MOO input Rds", + "description": "File path to the input multiOmicDataSet (MOO) RDS file.", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "parameters": [ + { + "key": "output_dir", + "displayName": "Output Directory", + "description": "Directory where properties will be written (sample_metadata.csv, feature_annotation.csv, counts/, analyses/).", + "paramType": "STRING", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": "moo", + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "outputDatasetName": "multiOmicDataSet Properties", + "outputs": { + "sample_metadata": { + "type": "file", + "name": "sample_metadata.csv" + }, + "feature_annotation": { + "type": "file", + "name": "feature_annotation.csv" + }, + "counts": { + "type": "directory", + "name": "counts/" + }, + "analyses": { + "type": "directory", + "name": "analyses/" + } + } +} \ No newline at end of file diff --git a/code/MOSuite/inst/extdata/galaxy/2_blueprints/batch_correct_counts.json b/code/MOSuite/inst/extdata/galaxy/2_blueprints/batch_correct_counts.json new file mode 100644 index 0000000..006f336 --- /dev/null +++ b/code/MOSuite/inst/extdata/galaxy/2_blueprints/batch_correct_counts.json @@ -0,0 +1,161 @@ +{ + "r_function": "batch_correct_counts", + "title": "Batch Correction\n", + "description": "Perform batch correction using sva::ComBat()\n", + "columns": [ + { + "key": "feature_id_colname", + "displayName": "Feature ID Column", + "description": "The column from the counts data containing the Feature IDs (Usually Gene or Protein ID).\nThis is usually the first column of your input Counts Matrix. Only columns of Text type from your input Counts\nMatrix will be available to select for this parameter. (Default: `NULL` - first column in the counts matrix will be\nused.)\n", + "paramGroup": "Basic", + "sourceDataset": "counts_matrix", + "columnType": "STRING", + "isMulti": null + }, + { + "key": "samples_to_include", + "displayName": "Columns to Include", + "description": "Which samples would you like to include? Usually, you will choose all sample columns, or\nyou could choose to remove certain samples. Samples excluded here will be removed in this step and from further\nanalysis downstream of this step. (Default: `NULL` - all sample IDs in `moo@sample_meta` will be used.)\n", + "paramGroup": "Basic", + "sourceDataset": "counts_matrix", + "columnType": "ALL", + "isMulti": true + }, + { + "key": "sample_id_colname", + "displayName": "Sample Names Column", + "description": "The column from the sample metadata containing the sample names. The names in this column\nmust exactly match the names used as the sample column names of your input Counts Matrix. (Default: `NULL` - first\ncolumn in the sample metadata will be used.)\n", + "paramGroup": "Basic", + "sourceDataset": "sample_metadata", + "columnType": "STRING", + "isMulti": null + }, + { + "key": "covariates_colnames", + "displayName": "Covariates", + "description": "The column name(s) from the sample metadata\ncontaining variable(s) of interest, such as phenotype.\nMost commonly this will be the same column selected for your Groups Column.\nSome experimental designs may require that you add additional covariate columns here.\nDo not include the `batch_colname` here.\n", + "paramGroup": "Basic", + "sourceDataset": "sample_metadata", + "defaultValue": "Group", + "columnType": "ALL", + "isMulti": true + }, + { + "key": "batch_colname", + "displayName": "Batch Column", + "description": "The column from the sample metadata containing the batch information.\nSamples extracted, prepared, or sequenced at separate times or using separate materials/staff/equipment\nmay belong to different batches.\nNot all data sets have batches, in which case you do not need batch correction.\nIf your data set has no batches, you can provide a batch column with the same\nvalue in every row to skip batch correction (alternatively, simply do not run this function).\n", + "paramGroup": "Basic", + "sourceDataset": "sample_metadata", + "defaultValue": "Batch", + "columnType": "ALL", + "isMulti": null + }, + { + "key": "label_colname", + "displayName": "Labels Column", + "description": "The column from the sample metadata containing the sample labels as you wish them to appear in\nthe plots produced by this template. This can be the same Sample Names Column. However, you may desire different\nlabels to display on your figure (e.g. shorter labels are sometimes preferred on plots). In that case, select the\ncolumn with your preferred Labels here. The selected column should contain unique names for each sample. (Default:\n`NULL` -- `sample_id_colname` will be used.)\n", + "paramGroup": "Basic", + "sourceDataset": "sample_metadata", + "columnType": "ALL", + "isMulti": null + } + ], + "inputDatasets": [ + { + "key": "moo_input_rds", + "displayName": "MOO input Rds", + "description": "File path to read the input multiOmicDataSet object (MOO)", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "parameters": [ + { + "key": "moo_output_rds", + "displayName": "MOO output Rds", + "description": "File path to output the multiOmicDataSet object (MOO) as an Rds file at the end of the function", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "count_type", + "displayName": "Count Type", + "description": "the type of counts to use -- must be a name in the counts slot (`moo@counts`)\n", + "paramType": "STRING", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": "norm", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "sub_count_type", + "displayName": "Sub Count Type", + "description": "if `count_type` is a list, specify the sub count type within the list. (Default: `\"voom\"`)\n", + "paramType": "STRING", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": "voom", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "colors_for_plots", + "displayName": "Colors for plots", + "description": "Colors for the PCA and histogram will be picked, in order, from this list.\nColors must either be names in `grDevices::colors()` or valid hex codes.\n", + "paramType": "MULTISELECT", + "paramGroup": "Visualization", + "paramValues": [ + "#5954d6", + "#e1562c", + "#b80058", + "#00c6f8", + "#d163e6", + "#00a76c", + "#ff9287", + "#008cf9", + "#006e00", + "#796880", + "#FFA500", + "#878500" + ], + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "save_plots", + "displayName": "Save Plots", + "description": "Whether to save plots to files during analysis (Defaults to `TRUE`, overwritable using option 'moo_save_plots' or environment variable 'MOO_SAVE_PLOTS')\n", + "paramType": "BOOLEAN", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "outputs": { + "multiOmicDataSet": { + "type": "file", + "name": "moo.rds" + }, + "figures": { + "type": "directory", + "name": "figures/batch/" + } + } +} diff --git a/code/MOSuite/inst/extdata/galaxy/2_blueprints/clean_raw_counts.json b/code/MOSuite/inst/extdata/galaxy/2_blueprints/clean_raw_counts.json new file mode 100644 index 0000000..7f5c144 --- /dev/null +++ b/code/MOSuite/inst/extdata/galaxy/2_blueprints/clean_raw_counts.json @@ -0,0 +1,156 @@ +{ + "r_function": "clean_raw_counts", + "title": "Clean Raw Counts\n", + "description": "This function checks the input raw counts matrix for common formatting problems with feature identifiers and sample\nnames. If feature IDs contain multiple IDs separated by special characters (| - , or space) they will be split into\nmultiple columns. If duplicate feature IDs are detected the counts are summed across duplicate feature ID rows\nwithin each sample. Invalid sample names will also be reported and can be automatically\ncorrected. If your sample names are corrected here, be sure to make equivalent changes to your metadata table.\n", + "columns": [ + { + "key": "feature_id_colname", + "displayName": "Feature ID Column", + "description": "The column from the counts data containing the Feature IDs (Usually Gene or Protein ID).\nThis is usually the first column of your input Counts Matrix. Only columns of Text type from your input Counts\nMatrix will be available to select for this parameter. (Default: `NULL` - first column in the counts matrix will be\nused.)\n", + "paramGroup": "Basic", + "sourceDataset": "moo@counts", + "columnType": "STRING", + "isMulti": null + }, + { + "key": "sample_id_colname", + "displayName": "Sample ID Column", + "description": "The column from the sample metadata containing the sample names. The names in this column\nmust exactly match the names used as the sample column names of your input Counts Matrix. (Default: `NULL` - first\ncolumn in the sample metadata will be used.)\n", + "paramGroup": "Basic", + "sourceDataset": "moo@sample_meta", + "columnType": "STRING", + "isMulti": null + } + ], + "inputDatasets": [ + { + "key": "moo_input_rds", + "displayName": "MOO input Rds", + "description": "File path to read the input multiOmicDataSet object (MOO)", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "parameters": [ + { + "key": "moo_output_rds", + "displayName": "MOO output Rds", + "description": "File path to output the multiOmicDataSet object (MOO) as an Rds file at the end of the function", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "count_type", + "displayName": "Count Type", + "description": "the type of counts to use -- must be a name in the counts slot (`moo@counts`)\n", + "paramType": "STRING", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": "raw", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "samples_to_rename", + "displayName": "Samples to Rename", + "description": "If you do not have a Plot Labels Column in your sample metadata table, you can use this\nparameter to rename samples manually for display on the PCA plot. Use \"Add item\" to add each additional sample for\nrenaming. Use the following format to describe which old name (in your sample metadata table) you want to rename to\nwhich new name: old_name: new_name\n", + "paramType": "VECTOR", + "paramGroup": "Advanced", + "paramValues": null, + "defaultValue": "", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "cleanup_column_names", + "displayName": "Cleanup Column Names", + "description": "Invalid raw counts column names can cause errors\nin the downstream analysis. If this is `TRUE`, any invalid column names\nwill be automatically altered to a correct format. These format changes\nwill include adding an \"X\" as the first character in any column name that\nbegan with a numeral and replacing some special characters (\"-,:. \") with\nunderscores (\"_\"). Invalid sample names and any changes made will be\ndetailed.\n", + "paramType": "BOOLEAN", + "paramGroup": "Advanced", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "split_gene_name", + "displayName": "Split Feature ID", + "description": "If `TRUE`, split the gene name column by any of these special characters: `,|_-:`", + "paramType": "BOOLEAN", + "paramGroup": "Advanced", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "aggregate_rows_with_duplicate_gene_names", + "displayName": "Aggregate Rows with Duplicate Feature Names", + "description": "If a Feature ID (from the\n\"Cleanup Column Names\" parameter above) is found to be duplicated on\nmultiple rows of the raw counts, the Log will report these Feature IDs.\nUsing the default behavior (`TRUE`), the counts for all rows with a\nduplicate Feature IDs are aggregated into a single row. Counts are summed\nacross duplicate Feature ID rows within each sample. Additional identifier\ncolumns, if present (e.g. Ensembl IDs), will be preserved and multiple\nmatching identifiers in such additional columns will appear as\ncomma-separated values in an aggregated row.\n", + "paramType": "BOOLEAN", + "paramGroup": "Advanced", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "gene_name_column_to_use_for_collapsing_duplicates", + "displayName": "Column Used to Aggregate Duplicates Feature IDs", + "description": "Select the column\nwith Feature IDs to use as grouping elements to collapse the counts matrix.\nThe log output will list the columns available to identify duplicate row\nIDs in order to aggregate information.\nIf left blank your \"Feature ID\" Column will be used to Aggregate Rows. If\n\"Feature ID\" column can be split into multiple IDs the non Ensembl ID name\nwill be used to aggregate duplicate IDs. If \"Feature ID\" column does not\ncontain Ensembl IDs the split Feature IDs will be named 'Feature_id_1' and\n'Feature_id_2'. For this case an error will occur and you will have\nto manually enter the Column ID for this field.\n", + "paramType": "STRING", + "paramGroup": "Advanced", + "paramValues": [ + "Gene", + "Pepetide", + "Protein", + "Ensembl_ID", + "Ensembl_ID_version", + "Gene_id_1", + "Gene_id_2", + "Original Gene Column" + ], + "defaultValue": "", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "save_plots", + "displayName": "Save Plots", + "description": "Whether to save plots to files during analysis (Defaults to `TRUE`, overwritable using option 'moo_save_plots' or environment variable 'MOO_SAVE_PLOTS')\n", + "paramType": "BOOLEAN", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "outputs": { + "multiOmicDataSet": { + "type": "file", + "name": "moo.rds" + }, + "figures": { + "type": "directory", + "name": "figures/clean/" + } + } +} diff --git a/code/MOSuite/inst/extdata/galaxy/2_blueprints/create_multiOmicDataSet_from_files.json b/code/MOSuite/inst/extdata/galaxy/2_blueprints/create_multiOmicDataSet_from_files.json new file mode 100644 index 0000000..c20d116 --- /dev/null +++ b/code/MOSuite/inst/extdata/galaxy/2_blueprints/create_multiOmicDataSet_from_files.json @@ -0,0 +1,83 @@ +{ + "r_function": "create_multiOmicDataSet_from_files", + "title": "Create Multi-Omic Dataset from Files\n", + "description": "Construct a multiOmicDataSet object from text files (e.g. TSV, CSV).\n", + "columns": [], + "inputDatasets": [ + { + "key": "sample_meta_filepath", + "displayName": "", + "description": "path to text file with sample IDs and metadata for differential analysis.\n", + "paramType": "TABULAR", + "paramGroup": "basic", + "paramValues": null, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "feature_counts_filepath", + "displayName": "", + "description": "path to text file of expected feature counts (e.g. gene counts from RSEM).\n", + "paramType": "TABULAR", + "paramGroup": "basic", + "paramValues": null, + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "parameters": [ + { + "key": "moo_output_rds", + "displayName": "MOO output Rds", + "description": "File path to output the multiOmicDataSet object (MOO) as an Rds file", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "sample_id_colname", + "displayName": "", + "description": "name of the column in `sample_metadata` that contains the sample IDs. (Default: `NULL` -\nfirst column in the sample metadata will be used.)\n", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "feature_id_colname", + "displayName": "", + "description": "name of the column in `counts_dat` that contains feature/gene IDs. (Default: `NULL` - first\ncolumn in the count data will be used.)\n", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "delim", + "displayName": "", + "description": "Delimiter used in the input files. Any delimiter accepted by `readr::read_delim()` can be used.\nIf the files are in CSV format, set `delim = ','`; for TSV format, set `delim = '\\t'`.\n", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "outputs": { + "multiOmicDataSet": { + "type": "file", + "name": "moo.rds" + } + } +} diff --git a/code/MOSuite/inst/extdata/galaxy/2_blueprints/diff_counts.json b/code/MOSuite/inst/extdata/galaxy/2_blueprints/diff_counts.json new file mode 100644 index 0000000..dfbc40e --- /dev/null +++ b/code/MOSuite/inst/extdata/galaxy/2_blueprints/diff_counts.json @@ -0,0 +1,181 @@ +{ + "r_function": "diff_counts", + "title": "Differential Analysis\n", + "description": "Differential expression analysis\n", + "columns": [ + { + "key": "feature_id_colname", + "displayName": "Feature/Gene Names Column", + "description": "The column from the counts data containing the Feature IDs (Usually Gene or Protein ID).\nThis is usually the first column of your input Counts Matrix. Only columns of Text type from your input Counts\nMatrix will be available to select for this parameter. (Default: `NULL` - first column in the counts matrix will be\nused.)\n", + "paramGroup": "Basic", + "sourceDataset": "Counts_Matrix", + "columnType": "STRING", + "isMulti": null + }, + { + "key": "sample_id_colname", + "displayName": "Sample Names Column", + "description": "The column from the sample metadata containing the sample names. The names in this column\nmust exactly match the names used as the sample column names of your input Counts Matrix. (Default: `NULL` - first\ncolumn in the sample metadata will be used.)\n", + "paramGroup": "Basic", + "sourceDataset": "Sample_Metadata", + "columnType": "ALL", + "isMulti": null + }, + { + "key": "samples_to_include", + "displayName": "Columns to Include", + "description": "Which samples would you like to include? Usually, you will choose all sample columns, or\nyou could choose to remove certain samples. Samples excluded here will be removed in this step and from further\nanalysis downstream of this step. (Default: `NULL` - all sample IDs in `moo@sample_meta` will be used.)\n", + "paramGroup": "Basic", + "sourceDataset": "Counts_Matrix", + "columnType": "ALL", + "isMulti": true + }, + { + "key": "contrast_colname", + "displayName": "Contrast Variable Column", + "description": "The column in the metadata that contains the group variables you wish to find differential\nexpression between. Up to 2 columns (2-factor analysis) can be used.\n", + "paramGroup": "Basic", + "sourceDataset": "Sample_Metadata", + "columnType": "ALL", + "isMulti": true + }, + { + "key": "covariates_colnames", + "displayName": "Covariates Column(s)", + "description": "The column name(s) from the sample metadata containing variable(s) of interest, such as\nphenotype. Most commonly this will be the same column selected for your Groups Column. Some experimental designs\nmay require that you add additional covariate columns here.\n", + "paramGroup": "Basic", + "sourceDataset": "Sample_Metadata", + "columnType": "ALL", + "isMulti": true + } + ], + "inputDatasets": [ + { + "key": "moo_input_rds", + "displayName": "MOO input Rds", + "description": "File path to read the input multiOmicDataSet object (MOO)", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "parameters": [ + { + "key": "moo_output_rds", + "displayName": "MOO output Rds", + "description": "File path to output the multiOmicDataSet object (MOO) as an Rds file at the end of the function", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "count_type", + "displayName": "Count Type", + "description": "the type of counts to use -- must be a name in the counts slot (`moo@counts`)\n", + "paramType": "STRING", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": "filt", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "sub_count_type", + "displayName": "Sub Count Type", + "description": "if `count_type` is a list, specify the sub count type within the list. (Default: `NULL`)\n", + "paramType": "STRING", + "paramGroup": "Basic", + "paramValues": null, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "contrasts", + "displayName": "Contrasts", + "description": "Specify each contrast in the format group1-group2, e.g. treated-control\n", + "paramType": "VECTOR", + "paramGroup": "Basic", + "paramValues": null, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "input_in_log_counts", + "displayName": "Input in log Counts", + "description": "set this to `TRUE` if counts are already log2-transformed\n", + "paramType": "BOOLEAN", + "paramGroup": "Advanced", + "paramValues": null, + "defaultValue": false, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "return_mean_and_sd", + "displayName": "Return Mean and SD", + "description": "if TRUE, return Mean and Standard Deviation of groups in addition to DEG estimates for\ncontrast(s)\n", + "paramType": "BOOLEAN", + "paramGroup": "Advanced", + "paramValues": null, + "defaultValue": false, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "voom_normalization_method", + "displayName": "Normalization Method", + "description": "Normalization method to be applied to the logCPM values when using `limma::voom`", + "paramType": "SELECT", + "paramGroup": "Advanced", + "paramValues": [ + "none", + "scale", + "quantile", + "cyclicloess", + "TMM", + "TMMwzp", + "RLE", + "upperquartile" + ], + "defaultValue": "quantile", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "save_plots", + "displayName": "Save Plots", + "description": "Whether to save plots to files during analysis (Defaults to `TRUE`, overwritable using option 'moo_save_plots' or environment variable 'MOO_SAVE_PLOTS')\n", + "paramType": "BOOLEAN", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "outputs": { + "multiOmicDataSet": { + "type": "file", + "name": "moo.rds" + }, + "figures": { + "type": "directory", + "name": "figures/diff/" + } + } +} diff --git a/code/MOSuite/inst/extdata/galaxy/2_blueprints/filter_counts.json b/code/MOSuite/inst/extdata/galaxy/2_blueprints/filter_counts.json new file mode 100644 index 0000000..58d5f49 --- /dev/null +++ b/code/MOSuite/inst/extdata/galaxy/2_blueprints/filter_counts.json @@ -0,0 +1,427 @@ +{ + "r_function": "filter_counts", + "title": "Filter Low Counts\n", + "description": "This is often the first step in the QC portion of an analysis to filter out\nfeatures that have very low raw counts across most or all of your samples.\nThis function takes a multiOmicDataSet containing clean raw counts and a sample\nmetadata table, and returns the multiOmicDataSet object with filtered counts.\nIt also produces an image consisting of three QC plots.\nYou can tune the threshold for tuning how low counts for a given gene are\nbefore they are deemed \"too low\" and filtered out of downstream analysis. By\ndefault, this parameter is set to 1, meaning any raw count value less than 1\nwill count as \"too low\".\nThe QC plots are provided to help you assess: (1) PCA Plot: the within and\nbetween group variance in expression after dimensionality reduction; (2)\nCount Density Histogram: the dis/similarity of count distributions between\nsamples; and (3) Similarity Heatmap: the overall similarity of samples to one\nanother based on unsupervised clustering.\n", + "columns": [ + { + "key": "feature_id_colname", + "displayName": "Feature ID Column", + "description": "The column from the counts data containing the Feature IDs (Usually Gene or Protein ID).\nThis is usually the first column of your input Counts Matrix. Only columns of Text type from your input Counts\nMatrix will be available to select for this parameter. (Default: `NULL` - first column in the counts matrix will be\nused.)\n", + "paramGroup": "Basic", + "sourceDataset": "counts_matrix", + "columnType": "STRING", + "isMulti": null + }, + { + "key": "samples_to_include", + "displayName": "Columns to Include", + "description": "Which samples would you like to include? Usually, you will choose all sample columns, or\nyou could choose to remove certain samples. Samples excluded here will be removed in this step and from further\nanalysis downstream of this step. (Default: `NULL` - all sample IDs in `moo@sample_meta` will be used.)\n", + "paramGroup": "Basic", + "sourceDataset": "counts_matrix", + "columnType": "ALL", + "isMulti": true + }, + { + "key": "sample_id_colname", + "displayName": "Sample Names Column", + "description": "The column from the sample metadata containing the sample names. The names in this column\nmust exactly match the names used as the sample column names of your input Counts Matrix. (Default: `NULL` - first\ncolumn in the sample metadata will be used.)\n", + "paramGroup": "Basic", + "sourceDataset": "Sample_Metadata", + "columnType": "STRING", + "isMulti": null + }, + { + "key": "group_colname", + "displayName": "Groups Column", + "description": "The column from the sample metadata containing the sample group information. This is usually a\ncolumn showing to which experimental treatments each sample belongs (e.g. WildType, Knockout, Tumor, Normal,\nBefore, After, etc.).\n", + "paramGroup": "Basic", + "sourceDataset": "Sample_Metadata", + "defaultValue": "Group", + "columnType": "STRING", + "isMulti": null + }, + { + "key": "label_colname", + "displayName": "Labels Column", + "description": "The column from the sample metadata containing the sample labels as you wish them to appear in\nthe plots produced by this template. This can be the same Sample Names Column. However, you may desire different\nlabels to display on your figure (e.g. shorter labels are sometimes preferred on plots). In that case, select the\ncolumn with your preferred Labels here. The selected column should contain unique names for each sample. (Default:\n`NULL` -- `sample_id_colname` will be used.)\n", + "paramGroup": "Basic", + "sourceDataset": "Sample_Metadata", + "columnType": "ALL", + "isMulti": null + } + ], + "inputDatasets": [ + { + "key": "moo_input_rds", + "displayName": "MOO input Rds", + "description": "File path to read the input multiOmicDataSet object (MOO)", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "parameters": [ + { + "key": "moo_output_rds", + "displayName": "MOO output Rds", + "description": "File path to output the multiOmicDataSet object (MOO) as an Rds file at the end of the function", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "count_type", + "displayName": "Count Type", + "description": "the type of counts to use -- must be a name in the counts slot (`moo@counts`)\n", + "paramType": "STRING", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": "clean", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "use_cpm_counts_to_filter", + "displayName": "Use CPM Counts to filter", + "description": "If no transformation has been been performed on counts matrix (eg Raw Counts) set to\nTRUE. If TRUE counts will be transformed to CPM and filtered based on given criteria. If gene counts matrix has\nbeen transformed (eg log2, CPM, FPKM or some form of Normalization) set to FALSE. If FALSE no further\ntransformation will be applied and features will be filtered as is. For RNAseq data RAW counts should be\ntransformed to CPM in order to properly filter.\n", + "paramType": "BOOLEAN", + "paramGroup": "Filtering", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "minimum_count_value_to_be_considered_nonzero", + "displayName": "Minimum Count Value to be Considered Nonzero", + "description": "Minimum count value to be considered non-zero for a sample\n", + "paramType": "NUMBER", + "paramGroup": "Filtering", + "paramValues": null, + "defaultValue": 8, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "minimum_number_of_samples_with_nonzero_counts_in_total", + "displayName": "Minimum Number of Samples with Nonzero Counts in Total", + "description": "Minimum number of samples (total) with non-zero counts\n", + "paramType": "NUMBER", + "paramGroup": "Filtering", + "paramValues": null, + "defaultValue": 7, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "use_group_based_filtering", + "displayName": "Use Group-Based Filtering", + "description": "If TRUE, only keeps features (e.g. genes) that have at least a certain number of\nsamples with nonzero CPM counts in at least one group\n", + "paramType": "BOOLEAN", + "paramGroup": "Filtering", + "paramValues": null, + "defaultValue": false, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "minimum_number_of_samples_with_nonzero_counts_in_a_group", + "displayName": "Minimum Number of Samples with Nonzero Counts in a Group", + "description": "Only keeps genes that have at least this number of\nsamples with nonzero CPM counts in at least one group\n", + "paramType": "NUMBER", + "paramGroup": "Filtering", + "paramValues": null, + "defaultValue": 3, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "principal_component_on_x_axis", + "displayName": "Principal Component on X-axis", + "description": "The principal component to plot on the x-axis for the PCA plot. Choices include\n1, 2, 3, ... (default: 1)\n", + "paramType": "NUMBER", + "paramGroup": "PCA", + "paramValues": null, + "defaultValue": 1, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "principal_component_on_y_axis", + "displayName": "Principal Component on Y-axis", + "description": "The principal component to plot on the y-axis for the PCA plot. Choices include\n1, 2, 3, ... (default: 2)\n", + "paramType": "NUMBER", + "paramGroup": "PCA", + "paramValues": null, + "defaultValue": 2, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "legend_position_for_pca", + "displayName": "Legend Position for PCA", + "description": "legend position for the PCA plot\n", + "paramType": "SELECT", + "paramGroup": "PCA", + "paramValues": [ + "top", + "bottom", + "left", + "right", + "none" + ], + "defaultValue": "top", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "point_size_for_pca", + "displayName": "Point Size for PCA", + "description": "geom point size for the PCA plot\n", + "paramType": "NUMBER", + "paramGroup": "PCA", + "paramValues": null, + "defaultValue": 1, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "add_label_to_pca", + "displayName": "Add Labels to PCA", + "description": "label points on the PCA plot\n", + "paramType": "BOOLEAN", + "paramGroup": "PCA", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "label_font_size", + "displayName": "Label Font Size for PCA", + "description": "label font size for the PCA plot\n", + "paramType": "NUMBER", + "paramGroup": "PCA", + "paramValues": null, + "defaultValue": 3, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "label_offset_x_", + "displayName": "Label Offset (x)", + "description": "label offset x for the PCA plot\n", + "paramType": "NUMBER", + "paramGroup": "PCA", + "paramValues": null, + "defaultValue": 2, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "label_offset_y_", + "displayName": "Label Offset (Y)", + "description": "label offset y for the PCA plot\n", + "paramType": "NUMBER", + "paramGroup": "PCA", + "paramValues": null, + "defaultValue": 2, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "samples_to_rename", + "displayName": "Samples to Rename Manually on PCA", + "description": "If you do not have a Plot Labels Column in your sample metadata table, you can use this\nparameter to rename samples manually for display on the PCA plot. Use \"Add item\" to add each additional sample for\nrenaming. Use the following format to describe which old name (in your sample metadata table) you want to rename to\nwhich new name: old_name: new_name\n", + "paramType": "VECTOR", + "paramGroup": "PCA", + "paramValues": null, + "defaultValue": "", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "color_histogram_by_group", + "displayName": "Color Histogram by Group", + "description": "Set to FALSE to label histogram by Sample Names, or set to TRUE to label histogram by\nthe column you select in the \"Group Column Used to Color Histogram\" parameter (below). Default is FALSE.\n", + "paramType": "BOOLEAN", + "paramGroup": "Histogram", + "paramValues": null, + "defaultValue": false, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "set_min_max_for_x_axis_for_histogram", + "displayName": "Set Min/Max for X-axis for Histogram", + "description": "whether to set min/max value for histogram x-axis\n", + "paramType": "BOOLEAN", + "paramGroup": "Histogram", + "paramValues": null, + "defaultValue": false, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "minimum_for_x_axis_for_histogram", + "displayName": "Minimum for X-axis for Histogram", + "description": "x-axis minimum for histogram plot\n", + "paramType": "NUMBER", + "paramGroup": "Histogram", + "paramValues": null, + "defaultValue": -1, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "maximum_for_x_axis_for_histogram", + "displayName": "Maximum for X-axis for Histogram", + "description": "x-axis maximum for histogram plot\n", + "paramType": "NUMBER", + "paramGroup": "Histogram", + "paramValues": null, + "defaultValue": 1, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "legend_font_size_for_histogram", + "displayName": "Legend Font Size for Histogram", + "description": "legend font size for the histogram plot\n", + "paramType": "NUMBER", + "paramGroup": "Histogram", + "paramValues": null, + "defaultValue": 10, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "legend_position_for_histogram", + "displayName": "Legend Position for Histogram", + "description": "legend position for the histogram plot. consider setting to 'none' for a large\nnumber of samples.\n", + "paramType": "SELECT", + "paramGroup": "Histogram", + "paramValues": [ + "right", + "bottom", + "left", + "top", + "none" + ], + "defaultValue": "top", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "number_of_histogram_legend_columns", + "displayName": "Number of Histogram Legend Columns", + "description": "number of columns for the histogram legend\n", + "paramType": "NUMBER", + "paramGroup": "Histogram", + "paramValues": null, + "defaultValue": 6, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "colors_for_plots", + "displayName": "Colors for Plots", + "description": "Colors for the PCA and histogram will be picked, in order, from this list.\nColors must either be names in `grDevices::colors()` or valid hex codes.\n", + "paramType": "MULTISELECT", + "paramGroup": "Visualization", + "paramValues": [ + "#5954d6", + "#e1562c", + "#b80058", + "#00c6f8", + "#d163e6", + "#00a76c", + "#ff9287", + "#008cf9", + "#006e00", + "#796880", + "#FFA500", + "#878500" + ], + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "interactive_plots", + "displayName": "Interactive Plots", + "description": "set to TRUE to make PCA and Histogram plots interactive with `plotly`, allowing you to hover\nyour mouse over a point or line to view sample information. The similarity heat map will not display if this toggle\nis set to `TRUE`. Default is `FALSE`.\n", + "paramType": "BOOLEAN", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": false, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "plot_corr_matrix_heatmap", + "displayName": "Plot Correlation Matrix Heatmap", + "description": "Datasets with a large number of samples may be too large to create a correlation\nmatrix heatmap. If this function takes longer than 5 minutes to run, Set to `FALSE` and the correlation matrix will\nnot be be created. Default is `TRUE`.\n", + "paramType": "BOOLEAN", + "paramGroup": "TCGA", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "save_plots", + "displayName": "Save Plots", + "description": "Whether to save plots to files during analysis (Defaults to `TRUE`, overwritable using option 'moo_save_plots' or environment variable 'MOO_SAVE_PLOTS')\n", + "paramType": "BOOLEAN", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "outputs": { + "multiOmicDataSet": { + "type": "file", + "name": "moo.rds" + }, + "figures": { + "type": "directory", + "name": "figures/filt/" + } + } +} diff --git a/code/MOSuite/inst/extdata/galaxy/2_blueprints/filter_diff.json b/code/MOSuite/inst/extdata/galaxy/2_blueprints/filter_diff.json new file mode 100644 index 0000000..d1756e0 --- /dev/null +++ b/code/MOSuite/inst/extdata/galaxy/2_blueprints/filter_diff.json @@ -0,0 +1,345 @@ +{ + "r_function": "filter_diff", + "title": "Filter Differential Features\n", + "description": "Outputs dataset of significant genes from DEG table; filters genes based on statistical significance (p-value or\nadjusted p-value) and change (fold change, log2 fold change, or t-statistic); in addition allows for selection of DEG\nestimates and for sub-setting of contrasts and groups included in the output gene list.\n", + "columns": [ + { + "key": "feature_id_colname", + "displayName": "Gene Names Column", + "description": "The column from the counts data containing the Feature IDs (Usually Gene or Protein ID).\nThis is usually the first column of your input Counts Matrix. Only columns of Text type from your input Counts\nMatrix will be available to select for this parameter. (Default: `NULL` - first column in the counts matrix will be\nused.)\n", + "paramGroup": "Basic", + "sourceDataset": "DEG_Table", + "columnType": "STRING", + "isMulti": null + } + ], + "inputDatasets": [ + { + "key": "moo_input_rds", + "displayName": "MOO input Rds", + "description": "File path to read the input multiOmicDataSet object (MOO)", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "parameters": [ + { + "key": "moo_output_rds", + "displayName": "MOO output Rds", + "description": "File path to output the multiOmicDataSet object (MOO) as an Rds file at the end of the function", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "significance_column", + "displayName": "Significance Column", + "description": "Column name for significance, e.g. `\"pval\"` or `\"pvaladj\"` (default)\n", + "paramType": "SELECT", + "paramGroup": "Basic", + "paramValues": [ + "adjpval", + "pval" + ], + "defaultValue": "adjpval", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "significance_cutoff", + "displayName": "Significance Cutoff", + "description": "Features will only be kept if their `significance_column` is less then this cutoff\nthreshold\n", + "paramType": "NUMBER", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": 0.05, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "change_column", + "displayName": "Change Column", + "description": "Column name for change, e.g. `\"logFC\"` (default)\n", + "paramType": "SELECT", + "paramGroup": "Basic", + "paramValues": [ + "FC", + "logFC", + "tstat" + ], + "defaultValue": "logFC", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "change_cutoff", + "displayName": "Change Cutoff", + "description": "Features will only be kept if the absolute value of their `change_column` is greater than or\nequal to this cutoff threshold\n", + "paramType": "NUMBER", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": 1, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "filtering_mode", + "displayName": "Filtering Mode", + "description": "Accepted values: `\"any\"` or `\"all\"` to include features that meet the criteria in *any*contrast or in *all* contrasts\n", + "paramType": "SELECT", + "paramGroup": "Basic", + "paramValues": [ + "any", + "all" + ], + "defaultValue": "any", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "include_estimates", + "displayName": "Include Estimates", + "description": "Column names of estimates to include. Default: `c(\"FC\", \"logFC\", \"tstat\", \"pval\", \"adjpval\")`", + "paramType": "MULTISELECT", + "paramGroup": "Advanced", + "paramValues": [ + "mean", + "sd", + "FC", + "logFC", + "tstat", + "pval", + "adjpval" + ], + "defaultValue": ["FC", "logFC", "tstat", "pval", "adjpval"], + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "round_estimates", + "displayName": "Round Estimates", + "description": "Whether to round estimates. Default: `TRUE`", + "paramType": "BOOLEAN", + "paramGroup": "Advanced", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "contrast_filter", + "displayName": "Contrasts Filter", + "description": "Whether to filter `contrasts` in or our of analysis. If `\"keep\"`, only the contrast names\nlisted in `contrasts` will be included. If `\"remove`, the contrast names listed by `contrasts` will be removed. If\n`\"none\"`, all contrasts in the dataset are used. Options: `\"keep\"`, `\"remove\"`, or `\"none\"`", + "paramType": "SELECT", + "paramGroup": "Filter", + "paramValues": [ + "none", + "keep", + "remove" + ], + "defaultValue": "none", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "contrasts", + "displayName": "Contrasts", + "description": "Contrast names to filter by `contrast_filter`. If `contrast_filter` is `\"none\"`, this parameter has\nno effect.\n", + "paramType": "VECTOR", + "paramGroup": "Filter", + "paramValues": null, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "groups_filter", + "displayName": "Groups Filter", + "description": "Whether to filter `groups` in or out of analysis. If `\"keep\"`, only the group names listed in\n`groups` will be included. If `\"remove\"`, the group names listed by `groups` will be removed. If `\"none\"`, all\ngroups in the dataset are used.\n", + "paramType": "SELECT", + "paramGroup": "Filter", + "paramValues": [ + "none", + "keep", + "remove" + ], + "defaultValue": "none", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "groups", + "displayName": "Groups", + "description": "Group names to filter by `groups_filter`. If `groups_filter` is `\"none\"`, this parameter has no effect.\nOptions: `\"keep\"`, `\"remove\"`, or `\"none\"`", + "paramType": "VECTOR", + "paramGroup": "Filter", + "paramValues": null, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "label_font_size", + "displayName": "Label Font Size", + "description": "Font size for labels in the plot (default: 6)\n", + "paramType": "NUMBER", + "paramGroup": "Label", + "paramValues": null, + "defaultValue": 6, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "label_distance", + "displayName": "Label Distance", + "description": "Distance of labels from the bars (default: 1)\n", + "paramType": "NUMBER", + "paramGroup": "Label", + "paramValues": null, + "defaultValue": 1, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "y_axis_expansion", + "displayName": "Y-Axis Expansion", + "description": "Expansion of the y-axis (default: 0.08)\n", + "paramType": "NUMBER", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": 0.08, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "fill_colors", + "displayName": "Fill Colors ", + "description": "Fill colors for the bars (default: c(\"steelblue1\", \"whitesmoke\"))\n", + "paramType": "MULTISELECT", + "paramGroup": "Visualization", + "paramValues": [ + "aliceblue", + "antiquewhite4", + "darkorange", + "gold", + "red3", + "springgreen", + "steelblue1", + "blue2", + "violetred3", + "whitesmoke", + "gray60", + "gray90", + "black", + "white" + ], + "defaultValue": ["steelblue1", "whitesmoke"], + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "pie_chart_in_3d", + "displayName": "Pie Chart in 3D", + "description": "Whether to draw pie charts in 3D (default: TRUE)\n", + "paramType": "BOOLEAN", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "bar_width", + "displayName": "Bar Width", + "description": "Width of the bars (default: 0.4)\n", + "paramType": "NUMBER", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": 0.4, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "draw_bar_border", + "displayName": "Draw Bar Border", + "description": "Whether to draw borders around bars (default: TRUE)\n", + "paramType": "BOOLEAN", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "rounding_decimal_for_percent_cells", + "displayName": "Rounding Decimal for Percent Calls", + "description": "Decimal place to use when rounding Percent cells\n", + "paramType": "NUMBER", + "paramGroup": "Advanced", + "paramValues": null, + "defaultValue": 0, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "plot_titles_fontsize", + "displayName": "Font Size for Plot Titles", + "description": "Font size for plot titles (default: 12)\n", + "paramType": "NUMBER", + "paramGroup": "Label", + "paramValues": null, + "defaultValue": 12, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "save_plots", + "displayName": "Save Plots", + "description": "Whether to save plots to files during analysis (Defaults to `TRUE`, overwritable using option 'moo_save_plots' or environment variable 'MOO_SAVE_PLOTS')\n", + "paramType": "BOOLEAN", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "outputs": { + "multiOmicDataSet": { + "type": "file", + "name": "moo.rds" + }, + "figures": { + "type": "directory", + "name": "figures/diff/filt/" + } + } +} diff --git a/code/MOSuite/inst/extdata/galaxy/2_blueprints/normalize_counts.json b/code/MOSuite/inst/extdata/galaxy/2_blueprints/normalize_counts.json new file mode 100644 index 0000000..118f7fe --- /dev/null +++ b/code/MOSuite/inst/extdata/galaxy/2_blueprints/normalize_counts.json @@ -0,0 +1,408 @@ +{ + "r_function": "normalize_counts", + "title": "Normalization\n", + "description": "Normalize counts\n", + "columns": [ + { + "key": "feature_id_colname", + "displayName": "Feature ID Column", + "description": "The column from the counts data containing the Feature IDs (Usually Gene or Protein ID).\nThis is usually the first column of your input Counts Matrix. Only columns of Text type from your input Counts\nMatrix will be available to select for this parameter. (Default: `NULL` - first column in the counts matrix will be\nused.)\n", + "paramGroup": "Basic", + "sourceDataset": "counts_matrix", + "columnType": "STRING", + "isMulti": null + }, + { + "key": "samples_to_include", + "displayName": "Columns to Include", + "description": "Which samples would you like to include? Usually, you will choose all sample columns, or\nyou could choose to remove certain samples. Samples excluded here will be removed in this step and from further\nanalysis downstream of this step. (Default: `NULL` - all sample IDs in `moo@sample_meta` will be used.)\n", + "paramGroup": "Basic", + "sourceDataset": "counts_matrix", + "columnType": "ALL", + "isMulti": true + }, + { + "key": "sample_id_colname", + "displayName": "Sample Names Column", + "description": "The column from the sample metadata containing the sample names. The names in this column\nmust exactly match the names used as the sample column names of your input Counts Matrix. (Default: `NULL` - first\ncolumn in the sample metadata will be used.)\n", + "paramGroup": "Basic", + "sourceDataset": "Sample_Metadata", + "columnType": "STRING", + "isMulti": null + }, + { + "key": "group_colname", + "displayName": "Groups Column", + "description": "The column from the sample metadata containing the sample group information. This is usually a\ncolumn showing to which experimental treatments each sample belongs (e.g. WildType, Knockout, Tumor, Normal,\nBefore, After, etc.).\n", + "paramGroup": "Basic", + "sourceDataset": "Sample_Metadata", + "defaultValue": "Group", + "columnType": "ALL", + "isMulti": null + }, + { + "key": "label_colname", + "displayName": "Labels Column", + "description": "The column from the sample metadata containing the sample labels as you wish them to appear in\nthe plots produced by this template. This can be the same Sample Names Column. However, you may desire different\nlabels to display on your figure (e.g. shorter labels are sometimes preferred on plots). In that case, select the\ncolumn with your preferred Labels here. The selected column should contain unique names for each sample. (Default:\n`NULL` -- `sample_id_colname` will be used.)\n", + "paramGroup": "Basic", + "sourceDataset": "Sample_Metadata", + "columnType": "ALL", + "isMulti": null + } + ], + "inputDatasets": [ + { + "key": "moo_input_rds", + "displayName": "MOO input Rds", + "description": "File path to read the input multiOmicDataSet object (MOO)", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "parameters": [ + { + "key": "moo_output_rds", + "displayName": "MOO output Rds", + "description": "File path to output the multiOmicDataSet object (MOO) as an Rds file at the end of the function", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "count_type", + "displayName": "Count Type", + "description": "the type of counts to use -- must be a name in the counts slot (`moo@counts`)\n", + "paramType": "STRING", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": "filt", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "norm_type", + "displayName": "Normalization Type", + "description": "normalization type. Default: \"voom\" which uses `limma::voom`.\n", + "paramType": "STRING", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": "voom", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "input_in_log_counts", + "displayName": "Input in Log Counts", + "description": "set this to `TRUE` if counts are already log2-transformed\n", + "paramType": "BOOLEAN", + "paramGroup": "Normalization", + "paramValues": null, + "defaultValue": false, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "voom_normalization_method", + "displayName": "Normalization Method", + "description": "Normalization method to be applied to the logCPM values when using `limma::voom`", + "paramType": "SELECT", + "paramGroup": "Normalization", + "paramValues": [ + "none", + "scale", + "quantile", + "cyclicloess" + ], + "defaultValue": "quantile", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "samples_to_rename", + "displayName": "Samples to Rename Manually on PCA", + "description": "If you do not have a Plot Labels Column in your sample metadata table, you can use this\nparameter to rename samples manually for display on the PCA plot. Use \"Add item\" to add each additional sample for\nrenaming. Use the following format to describe which old name (in your sample metadata table) you want to rename to\nwhich new name: old_name: new_name\n", + "paramType": "VECTOR", + "paramGroup": "PCA", + "paramValues": null, + "defaultValue": "", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "add_label_to_pca", + "displayName": "Add Labels to PCA", + "description": "label points on the PCA plot\n", + "paramType": "BOOLEAN", + "paramGroup": "PCA", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "principal_component_on_x_axis", + "displayName": "Principal Component on X-axis for PCA", + "description": "The principal component to plot on the x-axis for the PCA plot. Choices include\n1, 2, 3, ... (default: 1)\n", + "paramType": "NUMBER", + "paramGroup": "PCA", + "paramValues": null, + "defaultValue": 1, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "principal_component_on_y_axis", + "displayName": "Principal Component on Y-axis for PCA", + "description": "The principal component to plot on the y-axis for the PCA plot. Choices include\n1, 2, 3, ... (default: 2)\n", + "paramType": "NUMBER", + "paramGroup": "PCA", + "paramValues": null, + "defaultValue": 2, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "legend_position_for_pca", + "displayName": "Legend position for PCA", + "description": "legend position for the PCA plot\n", + "paramType": "SELECT", + "paramGroup": "PCA", + "paramValues": [ + "top", + "bottom", + "left", + "right", + "none" + ], + "defaultValue": "top", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "label_offset_x_", + "displayName": "Label Offset (x) for PCA", + "description": "label offset x for the PCA plot\n", + "paramType": "NUMBER", + "paramGroup": "PCA", + "paramValues": null, + "defaultValue": 2, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "label_offset_y_", + "displayName": "Label Offset (y) for PCA", + "description": "label offset y for the PCA plot\n", + "paramType": "NUMBER", + "paramGroup": "PCA", + "paramValues": null, + "defaultValue": 2, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "label_font_size", + "displayName": "Label Font Size for PCA", + "description": "label font size for the PCA plot\n", + "paramType": "NUMBER", + "paramGroup": "PCA", + "paramValues": null, + "defaultValue": 3, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "point_size_for_pca", + "displayName": "Point Size for PCA", + "description": "geom point size for the PCA plot\n", + "paramType": "NUMBER", + "paramGroup": "PCA", + "paramValues": null, + "defaultValue": 8, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "color_histogram_by_group", + "displayName": "Color Histogram by Group", + "description": "Set to FALSE to label histogram by Sample Names, or set to TRUE to label histogram by\nthe column you select in the \"Group Column Used to Color Histogram\" parameter (below). Default is FALSE.\n", + "paramType": "BOOLEAN", + "paramGroup": "Histogram", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "maximum_for_x_axis_for_histogram", + "displayName": "Maximum for X-axis in Histogram", + "description": "x-axis maximum for histogram plot\n", + "paramType": "NUMBER", + "paramGroup": "Histogram", + "paramValues": null, + "defaultValue": 1, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "minimum_for_x_axis_for_histogram", + "displayName": "Minimum for X-axis in Histogram", + "description": "x-axis minimum for histogram plot\n", + "paramType": "NUMBER", + "paramGroup": "Histogram", + "paramValues": null, + "defaultValue": -1, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "set_min_max_for_x_axis_for_histogram", + "displayName": "Set Min/Max for X-axis for Histogram", + "description": "whether to set min/max value for histogram x-axis\n", + "paramType": "BOOLEAN", + "paramGroup": "Histogram", + "paramValues": null, + "defaultValue": false, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "legend_font_size_for_histogram", + "displayName": "Legend Font Size for Histogram", + "description": "legend font size for the histogram plot\n", + "paramType": "NUMBER", + "paramGroup": "Histogram", + "paramValues": null, + "defaultValue": 10, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "legend_position_for_histogram", + "displayName": "Legend Position for Histogram", + "description": "legend position for the histogram plot. consider setting to 'none' for a large\nnumber of samples.\n", + "paramType": "SELECT", + "paramGroup": "Histogram", + "paramValues": [ + "top", + "bottom", + "left", + "right", + "none" + ], + "defaultValue": "top", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "number_of_histogram_legend_columns", + "displayName": "Number of Histogram Legend Columns", + "description": "number of columns for the histogram legend\n", + "paramType": "NUMBER", + "paramGroup": "Histogram", + "paramValues": null, + "defaultValue": 6, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "colors_for_plots", + "displayName": "Colors for Plots", + "description": "Colors for the PCA and histogram will be picked, in order, from this list.\nColors must either be names in `grDevices::colors()` or valid hex codes.\n", + "paramType": "MULTISELECT", + "paramGroup": "Visualization", + "paramValues": [ + "#5954d6", + "#e1562c", + "#b80058", + "#00c6f8", + "#d163e6", + "#00a76c", + "#ff9287", + "#008cf9", + "#006e00", + "#796880", + "#FFA500", + "#878500" + ], + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "interactive_plots", + "displayName": "Make Plots Interactive", + "description": "set to TRUE to make PCA and Histogram plots interactive with `plotly`, allowing you to hover\nyour mouse over a point or line to view sample information. The similarity heat map will not display if this toggle\nis set to `TRUE`. Default is `FALSE`.\n", + "paramType": "BOOLEAN", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": false, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "plot_corr_matrix_heatmap", + "displayName": "Plot Correlation Matrix Heatmap", + "description": "Datasets with a large number of samples may be too large to create a correlation\nmatrix heatmap. If this function takes longer than 5 minutes to run, Set to `FALSE` and the correlation matrix will\nnot be be created. Default is `TRUE`.\n", + "paramType": "BOOLEAN", + "paramGroup": "TCGA", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "save_plots", + "displayName": "Save Plots", + "description": "Whether to save plots to files during analysis (Defaults to `TRUE`, overwritable using option 'moo_save_plots' or environment variable 'MOO_SAVE_PLOTS')\n", + "paramType": "BOOLEAN", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "outputs": { + "multiOmicDataSet": { + "type": "file", + "name": "moo.rds" + }, + "figures": { + "type": "directory", + "name": "figures/norm/" + } + } +} diff --git a/code/MOSuite/inst/extdata/galaxy/2_blueprints/plot_expr_heatmap.json b/code/MOSuite/inst/extdata/galaxy/2_blueprints/plot_expr_heatmap.json new file mode 100644 index 0000000..5d77de0 --- /dev/null +++ b/code/MOSuite/inst/extdata/galaxy/2_blueprints/plot_expr_heatmap.json @@ -0,0 +1,558 @@ +{ + "r_function": "plot_expr_heatmap", + "title": "Plot Expression Heatmap\n", + "description": "The samples (i.e. the columns) are clustered in an unsupervised fashion based\non how similar their expression profiles are across the included genes. This\ncan help identify samples that are non clustering with their group as you\nmight expect based on the experimental design.\nBy default, the top 500 genes by variance are used, as these are\ngenerally going to include those genes that most distinguish your samples\nfrom one another. You can change this as well as many other parameters about\nthis heatmap if you explore the advanced options.\n", + "columns": [ + { + "key": "feature_id_colname", + "displayName": "Gene Column Name", + "description": "The column from the counts dataa containing the Feature IDs (Usually Gene or Protein ID).\nThis is usually the first column of your input Counts Matrix. Only columns of Text type from your input Counts\nMatrix will be available to select for this parameter. (Default: `NULL` - first column in the counts matrix will be\nused.)\n", + "paramGroup": "Data Setup", + "sourceDataset": "Counts_Matrix", + "columnType": "STRING", + "isMulti": null + }, + { + "key": "sample_id_colname", + "displayName": "Sample Name Column", + "description": "The column from the sample metadata containing the sample names. The names in this column\nmust exactly match the names used as the sample column names of your input Counts Matrix. (Default: `NULL` - first\ncolumn in the sample metadata will be used.)\n", + "paramGroup": "Data Setup", + "sourceDataset": "Sample_Metadata", + "columnType": "ALL", + "isMulti": null + }, + { + "key": "label_colname", + "displayName": "Sample Labels Column", + "description": "The column from the sample metadata containing the sample labels as you wish them to appear in\nthe plots produced by this template. This can be the same Sample Names Column. However, you may desire different\nlabels to display on your figure (e.g. shorter labels are sometimes preferred on plots). In that case, select the\ncolumn with your preferred Labels here. The selected column should contain unique names for each sample. (Default:\n`NULL` -- `sample_id_colname` will be used.)\n", + "paramGroup": "Data Setup", + "sourceDataset": "Sample_Metadata", + "columnType": "ALL", + "isMulti": null + }, + { + "key": "samples_to_include", + "displayName": "Samples to Include", + "description": "Which samples would you like to include? Usually, you will choose all sample columns, or\nyou could choose to remove certain samples. Samples excluded here will be removed in this step and from further\nanalysis downstream of this step. (Default: `NULL` - all sample IDs in `moo@sample_meta` will be used.)\n", + "paramGroup": "Data Setup", + "sourceDataset": "Counts_Matrix", + "columnType": "NUMBER", + "isMulti": true + }, + { + "key": "reorder_dendrogram_order", + "displayName": "Reorder Sample Dendrogram Order", + "description": "Reorder the samples (columns) of the dendrogram by name, e.g.\n“sample2”,“sample3\",“sample1\".\n", + "paramGroup": "Sample", + "sourceDataset": "Counts_Matrix", + "columnType": "ALL", + "isMulti": true + }, + { + "key": "group_colname", + "displayName": "Group Columns", + "description": "The column from the sample metadata containing the sample group information. This is usually a\ncolumn showing to which experimental treatments each sample belongs (e.g. WildType, Knockout, Tumor, Normal,\nBefore, After, etc.).\n", + "paramGroup": "Annotation", + "sourceDataset": "Sample_Metadata", + "defaultValue": "Group", + "columnType": "ALL", + "isMulti": true + } + ], + "inputDatasets": [ + { + "key": "moo_input_rds", + "displayName": "MOO input Rds", + "description": "File path to read the input multiOmicDataSet object (MOO)", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "parameters": [ + { + "key": "count_type", + "displayName": "Count Type", + "description": "the type of counts to use. Must be a name in the counts slot (`names(moo@counts)`).\n", + "paramType": "STRING", + "paramGroup": "Basic", + "paramValues": null, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "sub_count_type", + "displayName": "Sub Count Type", + "description": "used if `count_type` is a list in the counts slot: specify the sub count type within the list.\nMust be a name in `names(moo@counts[[count_type]])`.\n", + "paramType": "STRING", + "paramGroup": "Basic", + "paramValues": null, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "include_all_genes", + "displayName": "Include All Genes", + "description": "Set to TRUE if all genes are to be included. Set to FALSE if you want to filter genes by\nvariance and/or provide a list of specific genes that will appear in the heatmap.\n", + "paramType": "BOOLEAN", + "paramGroup": "Gene", + "paramValues": null, + "defaultValue": false, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "filter_top_genes_by_variance", + "displayName": "Filter Top Genes by Variance", + "description": "Set to TRUE if you want to only include the top genes by variance. Set to FALSE\nif you do not want to filter genes by variance.\n", + "paramType": "BOOLEAN", + "paramGroup": "Gene", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "top_genes_by_variance_to_include", + "displayName": "Top Genes by Variance to Include", + "description": "The number of genes to include if filtering genes by variance. This parameter\nis ignored if \"Filter top genes by variance\" is set to FALSE.\n", + "paramType": "NUMBER", + "paramGroup": "Gene", + "paramValues": null, + "defaultValue": 500, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "specific_genes_to_include_in_heatmap", + "displayName": "Specific Genes to Include in Heatmap", + "description": "Enter the gene symbols to be included in the heatmap, with each gene\nsymbol separated with a space from the others. Alternatively, paste in a column of gene names from any spreadsheet\napplication. This parameter is ignored if \"Include all genes\" is set to TRUE.\n", + "paramType": "STRING", + "paramGroup": "Gene", + "paramValues": null, + "defaultValue": "None", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "cluster_genes", + "displayName": "Cluster Genes", + "description": "Choose whether to cluster the rows (genes). If TRUE, rows will have clustering applied. If\nFALSE, clustering will not be applied to rows.\n", + "paramType": "BOOLEAN", + "paramGroup": "Gene", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "gene_clustering_method", + "displayName": "Gene Clustering Method", + "description": "Clustering method metric to be used in clustering samples. (TODO document options)\n", + "paramType": "SELECT", + "paramGroup": "Gene", + "paramValues": [ + "ward.D", + "ward.D2", + "single", + "complete", + "average", + "mcquitty", + "median", + "centroid" + ], + "defaultValue": "average", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "gene_distance_metric", + "displayName": "Gene Distance Metric", + "description": "Distance metric to be used in clustering genes. (TODO document options)\n", + "paramType": "SELECT", + "paramGroup": "Gene", + "paramValues": [ + "euclidean", + "maximum", + "manhattan", + "canberra", + "binary", + "minkowski", + "correlation" + ], + "defaultValue": "correlation", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "display_gene_dendrograms", + "displayName": "Display Gene Dendrogram", + "description": "Set to TRUE to show gene dendrograms. Set to FALSE to hide dendrograms.\n", + "paramType": "BOOLEAN", + "paramGroup": "Gene", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "display_gene_names", + "displayName": "Display Gene Names", + "description": "Set to TRUE to display gene names on the right side of the heatmap. Set to FALSE to hide\ngene names.\n", + "paramType": "BOOLEAN", + "paramGroup": "Gene", + "paramValues": null, + "defaultValue": false, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "center_and_rescale_expression", + "displayName": "Center and Rescale Expression", + "description": "Center and rescale expression for each gene across all included samples.\n", + "paramType": "BOOLEAN", + "paramGroup": "Gene", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "cluster_samples", + "displayName": "Cluster Samples", + "description": "Choose whether to cluster the columns (samples). If TRUE, columns will have clustering\napplied. If FALSE, clustering will not be applied to columns.\n", + "paramType": "BOOLEAN", + "paramGroup": "Sample", + "paramValues": null, + "defaultValue": false, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "arrange_sample_columns", + "displayName": "Arrange Sample Columns", + "description": "If TRUE, arranges columns by annotation groups. If FALSE, and \"Cluster Samples\" is\nFALSE, samples will appear in the order of input (samples to include)\n", + "paramType": "BOOLEAN", + "paramGroup": "Sample", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "order_by_gene_expression", + "displayName": "Order by Gene Expression", + "description": "If TRUE, set gene name below and direction for ordering\n", + "paramType": "BOOLEAN", + "paramGroup": "Sample", + "paramValues": null, + "defaultValue": false, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "gene_to_order_columns", + "displayName": "Gene to Order Columns", + "description": "Gene to order columns by expression levels\n", + "paramType": "STRING", + "paramGroup": "Sample", + "paramValues": null, + "defaultValue": " ", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "gene_expression_order", + "displayName": "Gene Expression Order", + "description": "Choose direction for gene order\n", + "paramType": "SELECT", + "paramGroup": "Sample", + "paramValues": [ + "low_to_high", + "high_to_low" + ], + "defaultValue": "low_to_high", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "smpl_clustering_method", + "displayName": "Sample Clustering Method", + "description": "Clustering method to be used in clustering samples. (TODO document options)\n", + "paramType": "SELECT", + "paramGroup": "Sample", + "paramValues": [ + "ward.D", + "ward.D2", + "single", + "complete", + "average", + "mcquitty", + "median", + "centroid" + ], + "defaultValue": "average", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "smpl_distance_metric", + "displayName": "Sample Distance Metric", + "description": "Distance metric to be used in clustering samples. (TODO document options)\n", + "paramType": "SELECT", + "paramGroup": "Sample", + "paramValues": [ + "euclidean", + "maximum", + "manhattan", + "canberra", + "binary", + "minkowski", + "correlation" + ], + "defaultValue": "correlation", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "display_smpl_dendrograms", + "displayName": "Display Sample Dendrograms", + "description": "Set to TRUE to show sample dendrograms. Set to FALSE to hide dendrogram.\n", + "paramType": "BOOLEAN", + "paramGroup": "Sample", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "reorder_dendrogram", + "displayName": "Reorder Sample Dendrogram", + "description": "If TRUE, set the order of the dendrogram (below)\n", + "paramType": "BOOLEAN", + "paramGroup": "Sample", + "paramValues": null, + "defaultValue": false, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "display_sample_names", + "displayName": "Display Sample Names", + "description": "Set to TRUE if you want sample names to be displayed on the plot. Set to FALSE to hide\nsample names.\n", + "paramType": "BOOLEAN", + "paramGroup": "Sample", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "assign_group_colors", + "displayName": "Assign Group Colors", + "description": "If TRUE, set the groups assigned colors (below)\n", + "paramType": "BOOLEAN", + "paramGroup": "Annotation", + "paramValues": null, + "defaultValue": false, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "assign_color_to_sample_groups", + "displayName": "Assign Color to Sample Groups", + "description": "Enter each sample to color in the format: group_name: color This parameter is\nignored if \"Assign Colors\" is set to FALSE.\n", + "paramType": "VECTOR", + "paramGroup": "Annotation", + "paramValues": null, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "group_colors", + "displayName": "Group Colors", + "description": "Set group annotation colors.\n", + "paramType": "MULTISELECT", + "paramGroup": "Annotation", + "paramValues": [ + "#5954d6", + "#e1562c", + "#b80058", + "#00c6f8", + "#d163e6", + "#00a76c", + "#ff9287", + "#008cf9", + "#006e00", + "#796880", + "#FFA500", + "#878500" + ], + "defaultValue": ["#5954d6", "#e1562c", "#b80058", "#00c6f8", "#d163e6", "#00a76c", "#ff9287", "#008cf9", "#006e00", "#796880", "#FFA500", "#878500"], + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "heatmap_color_scheme", + "displayName": "Heatmap Color Scheme", + "description": "color scheme (TODO document options)\n", + "paramType": "SELECT", + "paramGroup": "Visual", + "paramValues": [ + "Default", + "Blue to Red", + "Red to Vanilla", + "Violet to Pink", + "Bu Yl Rd", + "Bu Wt Rd" + ], + "defaultValue": "Default", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "autoscale_heatmap_color", + "displayName": "Autoscale Heatmap Color", + "description": "Set to TRUE to autoscale the heatmap colors between the maximum and minimum heatmap\ncolor parameters. If FALSE, set the heatmap colors between \"Set max heatmap color\" and \"Set min heatmap color\"\n(below).\n", + "paramType": "BOOLEAN", + "paramGroup": "Visual", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "set_max_heatmap_color", + "displayName": "Set Max Heatmap Color", + "description": "If Autoscale heatmap color is set to FALSE, set the maximum heatmap z-score value.\n", + "paramType": "NUMBER", + "paramGroup": "Visual", + "paramValues": null, + "defaultValue": 2, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "set_min_heatmap_color", + "displayName": "Set Min Heatmap Color", + "description": "If Autoscale heatmap color is set to FALSE, set the minimum heatmap z-score value\n", + "paramType": "NUMBER", + "paramGroup": "Visual", + "paramValues": null, + "defaultValue": -2, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "aspect_ratio", + "displayName": "Aspect Ratio", + "description": "Set figure Aspect Ratio. Ratio refers to entire figure including legend. If set to Auto figure\nsize is based on number of rows and columns form counts matrix. default - Auto\n", + "paramType": "STRING", + "paramGroup": "Visual", + "paramValues": null, + "defaultValue": "Auto", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "display_numbers", + "displayName": "Display Numbers", + "description": "Setting to FALSE (default) will not display numerical value of heat on heatmap. Set to TRUE if\nyou want to see these numbers on the plot.\n", + "paramType": "BOOLEAN", + "paramGroup": "Visual", + "paramValues": null, + "defaultValue": false, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "gene_name_font_size", + "displayName": "Gene Name Font Size", + "description": "Font size for gene names. If you don't want gene labels to show, toggle \"Display Gene\nNames\" below to FALSE\n", + "paramType": "NUMBER", + "paramGroup": "Visual", + "paramValues": null, + "defaultValue": 4, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "legend_font_size", + "displayName": "Legend Font Size", + "description": "Set Font size for figure legend. Default is 10.\n", + "paramType": "NUMBER", + "paramGroup": "Visual", + "paramValues": null, + "defaultValue": 10, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "sample_name_font_size", + "displayName": "Sample Name Font Size", + "description": "Font size for sample names. If you don't want to display samples names, toggle \"Display\nsample names\" (below) to FALSE\n", + "paramType": "NUMBER", + "paramGroup": "Visual", + "paramValues": null, + "defaultValue": 8, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "save_plots", + "displayName": "Save Plots", + "description": "Whether to save plots to files during analysis (Defaults to `TRUE`, overwritable using option 'moo_save_plots' or environment variable 'MOO_SAVE_PLOTS')\n", + "paramType": "BOOLEAN", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "outputs": { + "figures": { + "type": "file", + "name": "figures/heatmap/expr_heatmap.png" + } + } +} diff --git a/code/MOSuite/inst/extdata/galaxy/2_blueprints/plot_pca_2d.json b/code/MOSuite/inst/extdata/galaxy/2_blueprints/plot_pca_2d.json new file mode 100644 index 0000000..1655813 --- /dev/null +++ b/code/MOSuite/inst/extdata/galaxy/2_blueprints/plot_pca_2d.json @@ -0,0 +1,275 @@ +{ + "r_function": "plot_pca_2d", + "title": "PCA 2D\n", + "description": "Perform and plot a 2D Principal Components Analysis\nPerform and plot a 2D Principal Components Analysis\n", + "columns": [ + { + "key": "feature_id_colname", + "displayName": "FeatureID Name Column", + "description": "The column from the counts dataa containing the Feature IDs (Usually Gene or Protein ID).\nThis is usually the first column of your input Counts Matrix. Only columns of Text type from your input Counts\nMatrix will be available to select for this parameter. (Default: `NULL` - first column in the counts matrix will be\nused.)\n", + "paramGroup": "Basic", + "sourceDataset": "Counts_Matrix", + "columnType": "STRING", + "isMulti": null + }, + { + "key": "sample_id_colname", + "displayName": "Sample Names Column", + "description": "The column from the sample metadata containing the sample names. The names in this column\nmust exactly match the names used as the sample column names of your input Counts Matrix. (Default: `NULL` - first\ncolumn in the sample metadata will be used.)\n", + "paramGroup": "Basic", + "sourceDataset": "Sample_Metadata_Table", + "columnType": "STRING", + "isMulti": null + }, + { + "key": "group_colname", + "displayName": "Group Column", + "description": "The column from the sample metadata containing the sample group information. This is usually a\ncolumn showing to which experimental treatments each sample belongs (e.g. WildType, Knockout, Tumor, Normal,\nBefore, After, etc.).\n", + "paramGroup": "Basic", + "sourceDataset": "Sample_Metadata_Table", + "defaultValue": "Group", + "columnType": "ALL", + "isMulti": null + }, + { + "key": "label_colname", + "displayName": "Plot Labels Column", + "description": "The column from the sample metadata containing the sample labels as you wish them to appear in\nthe plots produced by this template. This can be the same Sample Names Column. However, you may desire different\nlabels to display on your figure (e.g. shorter labels are sometimes preferred on plots). In that case, select the\ncolumn with your preferred Labels here. The selected column should contain unique names for each sample. (Default:\n`NULL` -- `sample_id_colname` will be used.)\n", + "paramGroup": "Basic", + "sourceDataset": "Sample_Metadata_Table", + "defaultValue": "Label", + "columnType": "ALL", + "isMulti": null + } + ], + "inputDatasets": [ + { + "key": "moo_input_rds", + "displayName": "MOO input Rds", + "description": "File path to read the input multiOmicDataSet object (MOO)", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "parameters": [ + { + "key": "count_type", + "displayName": "Count Type", + "description": "type to assign the values of `counts_dat` to in the `counts` slot\n", + "paramType": "STRING", + "paramGroup": "Basic", + "paramValues": null, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "sub_count_type", + "displayName": "Sub Count Type", + "description": "used if `count_type` is a list in the counts slot: specify the sub count type within the list.\nMust be a name in `names(moo@counts[[count_type]])`.\n", + "paramType": "STRING", + "paramGroup": "Basic", + "paramValues": null, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "principal_components", + "displayName": "Principal Components", + "description": "vector with numbered principal components to plot\n", + "paramType": "MULTISELECT", + "paramGroup": "Basic", + "paramValues": [ + 1, + 2, + 3, + 4, + 5 + ], + "defaultValue": [1, 2], + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "point_size", + "displayName": "Point Size", + "description": "size for `ggplot2::geom_point()`", + "paramType": "NUMBER", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": 1, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "add_label", + "displayName": "Add Labels", + "description": "whether to add text labels for the points\n", + "paramType": "BOOLEAN", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "label_font_size", + "displayName": "Label Font Size", + "description": "label font size for the PCA plot\n", + "paramType": "NUMBER", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": 3, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "legend_position", + "displayName": "Legend Position", + "description": "passed to in `legend.position``ggplot2::theme()`", + "paramType": "SELECT", + "paramGroup": "Visualization", + "paramValues": [ + "top", + "bottom", + "left", + "right", + "none" + ], + "defaultValue": "top", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "color_values", + "displayName": "Color Values", + "description": "vector of colors as hex values or names recognized by R\n", + "paramType": "MULTISELECT", + "paramGroup": "Visualization", + "paramValues": [ + "slateblue3", + "tomato2", + "maroon", + "deepskyblue", + "mediumorchid2", + "mediumseagreen", + "salmon", + "dodgerblue", + "darkgreen", + "plum4", + "orange", + "yellow4", + "aquamarine3", + "salmon1", + "lightskyblue3", + "plum3", + "firebrick", + "darkolivegreen3", + "goldenrod1", + "burlywood2", + "gray70", + "firebrick2", + "steelblue", + "palegreen4", + "orchid4", + "darkorange1", + "yellow", + "sienna", + "palevioletred1", + "gray60", + "cyan4", + "darkorange3", + "mediumpurple3", + "violetred2", + "olivedrab", + "darkgoldenrod2", + "darkgoldenrod", + "gray40", + "palegreen3", + "thistle3", + "khaki1", + "deeppink2", + "chocolate3", + "paleturquoise3", + "wheat1", + "lightsteelblue", + "sandybrown", + "darkolivegreen2", + "thistle2", + "gray85", + "orchid3", + "darkseagreen1", + "lightgoldenrod1", + "lightskyblue2", + "dodgerblue3", + "darkseagreen3", + "forestgreen", + "lightpink2", + "mediumpurple4", + "lightpink1", + "thistle", + "navajowhite", + "lemonchiffon", + "bisque2", + "mistyrose", + "gray95", + "lightcyan3", + "peachpuff2", + "lightsteelblue2", + "lightyellow2", + "moccasin", + "antiquewhite2", + "gray80", + "lightgrey" + ], + "defaultValue": ["#5954d6", "#e1562c", "#b80058", "#00c6f8", "#d163e6", "#00a76c", "#ff9287", "#008cf9", "#006e00", "#796880", "#FFA500", "#878500"], + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "interactive_plots", + "displayName": "Interactive Plots", + "description": "set to TRUE to make PCA and Histogram plots interactive with `plotly`, allowing you to hover\nyour mouse over a point or line to view sample information. The similarity heat map will not display if this toggle\nis set to `TRUE`. Default is `FALSE`.\n", + "paramType": "BOOLEAN", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": false, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "save_plots", + "displayName": "Save Plots", + "description": "Whether to save plots to files during analysis (Defaults to `TRUE`, overwritable using option 'moo_save_plots' or environment variable 'MOO_SAVE_PLOTS')\n", + "paramType": "BOOLEAN", + "paramGroup": "Visualization", + "paramValues": [ + true, + false + ], + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "outputs": { + "figures": { + "type": "file", + "name": "figures/pca/pca_2D.png" + } + } +} diff --git a/code/MOSuite/inst/extdata/galaxy/2_blueprints/plot_pca_3d.json b/code/MOSuite/inst/extdata/galaxy/2_blueprints/plot_pca_3d.json new file mode 100644 index 0000000..54b06e8 --- /dev/null +++ b/code/MOSuite/inst/extdata/galaxy/2_blueprints/plot_pca_3d.json @@ -0,0 +1,212 @@ +{ + "r_function": "plot_pca_3d", + "title": "PCA 3D\n", + "description": "Perform and plot a 3D Principal Components Analysis\n3D PCA for counts dataframe\n", + "columns": [ + { + "key": "feature_id_colname", + "displayName": "FeatureID Name Column", + "description": "The column from the counts data containing feature IDs. If `NULL`, first column is used.\n", + "paramGroup": "Basic", + "sourceDataset": "Counts_Matrix", + "columnType": "STRING", + "isMulti": null + }, + { + "key": "sample_id_colname", + "displayName": "Sample Names Column", + "description": "The column from sample metadata containing sample names. If `NULL`, first column is used.\n", + "paramGroup": "Basic", + "sourceDataset": "Sample_Metadata_Table", + "columnType": "STRING", + "isMulti": null + }, + { + "key": "group_colname", + "displayName": "Group Column", + "description": "The column from sample metadata containing sample group information.\n", + "paramGroup": "Basic", + "sourceDataset": "Sample_Metadata_Table", + "defaultValue": "Group", + "columnType": "ALL", + "isMulti": null + }, + { + "key": "label_colname", + "displayName": "Plot Labels Column", + "description": "The column from sample metadata containing sample labels.\n", + "paramGroup": "Basic", + "sourceDataset": "Sample_Metadata_Table", + "defaultValue": "Label", + "columnType": "ALL", + "isMulti": null + } + ], + "inputDatasets": [ + { + "key": "moo_input_rds", + "displayName": "MOO input Rds", + "description": "File path to read the input multiOmicDataSet object (MOO)", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "parameters": [ + { + "key": "count_type", + "displayName": "Count Type", + "description": "the type of counts to use. Ignored when `moo_counts` is already a dataframe.\n", + "paramType": "STRING", + "paramGroup": "Basic", + "paramValues": null, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "sub_count_type", + "displayName": "Sub Count Type", + "description": "used if `count_type` is a list in the counts slot: specify the sub count type within the list.\n", + "paramType": "STRING", + "paramGroup": "Basic", + "paramValues": null, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "point_size", + "displayName": "Point Size", + "description": "size for `ggplot2::geom_point()`", + "paramType": "NUMBER", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": 8, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "color_values", + "displayName": "Color Values", + "description": "vector of colors as hex values or names recognized by R.\n", + "paramType": "MULTISELECT", + "paramGroup": "Visualization", + "paramValues": [ + "slateblue3", + "tomato2", + "maroon", + "deepskyblue", + "mediumorchid2", + "mediumseagreen", + "salmon", + "dodgerblue", + "darkgreen", + "plum4", + "orange", + "yellow4", + "aquamarine3", + "salmon1", + "lightskyblue3", + "plum3", + "firebrick", + "darkolivegreen3", + "goldenrod1", + "burlywood2", + "gray70", + "firebrick2", + "steelblue", + "palegreen4", + "orchid4", + "darkorange1", + "yellow", + "sienna", + "palevioletred1", + "gray60", + "cyan4", + "darkorange3", + "mediumpurple3", + "violetred2", + "olivedrab", + "darkgoldenrod2", + "darkgoldenrod", + "gray40", + "palegreen3", + "thistle3", + "khaki1", + "deeppink2", + "chocolate3", + "paleturquoise3", + "wheat1", + "lightsteelblue", + "sandybrown", + "darkolivegreen2", + "thistle2", + "gray85", + "orchid3", + "darkseagreen1", + "lightgoldenrod1", + "lightskyblue2", + "dodgerblue3", + "darkseagreen3", + "forestgreen", + "lightpink2", + "mediumpurple4", + "lightpink1", + "thistle", + "navajowhite", + "lemonchiffon", + "bisque2", + "mistyrose", + "gray95", + "lightcyan3", + "peachpuff2", + "lightsteelblue2", + "lightyellow2", + "moccasin", + "antiquewhite2", + "gray80", + "lightgrey" + ], + "defaultValue": ["#5954d6", "#e1562c", "#b80058", "#00c6f8", "#d163e6", "#00a76c", "#ff9287", "#008cf9", "#006e00", "#796880", "#FFA500", "#878500"], + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "plot_title", + "displayName": "Plot Title", + "description": "title for the plot\n", + "paramType": "STRING", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": "PCA 3D", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "save_plots", + "displayName": "Save Plots", + "description": "whether to save plot to disk.\n", + "paramType": "BOOLEAN", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "outputs": { + "figures": { + "type": "file", + "name": "figures/pca/pca_3D.html" + } + } +} diff --git a/code/MOSuite/inst/extdata/galaxy/2_blueprints/plot_venn_diagram.json b/code/MOSuite/inst/extdata/galaxy/2_blueprints/plot_venn_diagram.json new file mode 100644 index 0000000..9bda288 --- /dev/null +++ b/code/MOSuite/inst/extdata/galaxy/2_blueprints/plot_venn_diagram.json @@ -0,0 +1,1100 @@ +{ + "r_function": "plot_venn_diagram", + "title": "Venn Diagram\n", + "description": "Generates Venn diagram of intersections across a series of sets (e.g., intersections of significant genes across\ntested contrasts). This Venn diagram is available for up to five sets; Intersection plot is available for any number\nof sets. Specific sets can be selected for the visualizations and the returned dataset may include all (default) or\nspecified intersections.\nAn S7 generic with methods for \nlist(\"multiOmicDataSet\")\n and \nlist(\"data.frame\")\n.\n", + "columns": [ + { + "key": "feature_id_colname", + "displayName": "Elements Column", + "description": "The column from the counts data containing the Feature IDs (Usually Gene or Protein ID).\nThis is usually the first column of your input Counts Matrix. Only columns of Text type from your input Counts\nMatrix will be available to select for this parameter. (Default: `NULL` - first column in the counts matrix will be\nused.)\n", + "paramGroup": "Basic", + "sourceDataset": "Input_Dataset", + "columnType": "STRING", + "isMulti": null + }, + { + "key": "contrasts_colname", + "displayName": "Categories Column", + "description": "Name of the column in `moo_diff_summary_dat` that contains the contrast names (default:\n\"Contrast\")\n", + "paramGroup": "Basic", + "sourceDataset": "Input_Dataset", + "defaultValue": "Contrast", + "columnType": "STRING", + "isMulti": null + } + ], + "inputDatasets": [ + { + "key": "moo_input_rds", + "displayName": "DataFrame input Rds", + "description": "File path to read the summary dataframe (e.g. from plot_volcano_summary output)", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "summary_dataframe.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "parameters": [ + { + "key": "moo_output_rds", + "displayName": "Venn diagram DataFrame Rds", + "description": "File path to output the venn diagram DataFrame as an Rds file", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "select_contrasts", + "displayName": "Selected Categories", + "description": "A vector of contrast names to select for the plot. If empty, all contrasts are used.\n", + "paramType": "VECTOR", + "paramGroup": "Advanced", + "paramValues": null, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "plot_type", + "displayName": "Select Plot Type", + "description": "Type of plot to generate: \"Venn diagram\" or \"Intersection plot\". Default: \"Venn diagram\"\n", + "paramType": "SELECT", + "paramGroup": "Advanced", + "paramValues": [ + "Venn diagram", + "Intersection plot", + "Intersection table" + ], + "defaultValue": "Venn diagram", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "intersection_ids", + "displayName": "Intersection IDs", + "description": "A vector of intersection IDs to select for the plot. If empty, all intersections are used.\n", + "paramType": "VECTOR", + "paramGroup": "Advanced", + "paramValues": null, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "venn_force_unique", + "displayName": "Venn Force Unique", + "description": "If TRUE, forces unique elements in the Venn diagram. Default: TRUE\n", + "paramType": "BOOLEAN", + "paramGroup": "Venn Diagram", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "venn_numbers_format", + "displayName": "Venn Numbers Format", + "description": "Format for the numbers in the Venn diagram. Options: \"raw\", \"percent\", \"raw-percent\",\n\"percent-raw\". Default: \"raw\"\n", + "paramType": "SELECT", + "paramGroup": "Venn Diagram", + "paramValues": [ + "raw", + "percent", + "raw-percent", + "percent-raw" + ], + "defaultValue": "raw", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "venn_significant_digits", + "displayName": "Venn Significant Digits", + "description": "Number of significant digits for the Venn diagram numbers. Default: 2\n", + "paramType": "NUMBER", + "paramGroup": "Venn Diagram", + "paramValues": null, + "defaultValue": 2, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "venn_fill_colors", + "displayName": "Venn Fill Colors", + "description": "A vector of colors to fill the Venn diagram categories. Default: c(\"darkgoldenrod2\",\n\"darkolivegreen2\", \"mediumpurple3\", \"darkorange2\", \"lightgreen\")\n", + "paramType": "MULTISELECT", + "paramGroup": "Venn Diagram", + "paramValues": [ + "white", + "aliceblue", + "antiquewhite", + "antiquewhite1", + "antiquewhite2", + "antiquewhite3", + "antiquewhite4", + "aquamarine", + "aquamarine1", + "aquamarine2", + "aquamarine3", + "aquamarine4", + "azure", + "azure1", + "azure2", + "azure3", + "azure4", + "beige", + "bisque", + "bisque1", + "bisque2", + "bisque3", + "bisque4", + "black", + "blanchedalmond", + "blue", + "blue1", + "blue2", + "blue3", + "blue4", + "blueviolet", + "brown", + "brown1", + "brown2", + "brown3", + "brown4", + "burlywood", + "burlywood1", + "burlywood2", + "burlywood3", + "burlywood4", + "cadetblue", + "cadetblue1", + "cadetblue2", + "cadetblue3", + "cadetblue4", + "chartreuse", + "chartreuse1", + "chartreuse2", + "chartreuse3", + "chartreuse4", + "chocolate", + "chocolate1", + "chocolate2", + "chocolate3", + "chocolate4", + "coral", + "coral1", + "coral2", + "coral3", + "coral4", + "cornflowerblue", + "cornsilk", + "cornsilk1", + "cornsilk2", + "cornsilk3", + "cornsilk4", + "cyan", + "cyan1", + "cyan2", + "cyan3", + "cyan4", + "darkblue", + "darkcyan", + "darkgoldenrod", + "darkgoldenrod1", + "darkgoldenrod2", + "darkgoldenrod3", + "darkgoldenrod4", + "darkgray", + "darkgreen", + "darkgrey", + "darkkhaki", + "darkmagenta", + "darkolivegreen", + "darkolivegreen1", + "darkolivegreen2", + "darkolivegreen3", + "darkolivegreen4", + "darkorange", + "darkorange1", + "darkorange2", + "darkorange3", + "darkorange4", + "darkorchid", + "darkorchid1", + "darkorchid2", + "darkorchid3", + "darkorchid4", + "darkred", + "darksalmon", + "darkseagreen", + "darkseagreen1", + "darkseagreen2", + "darkseagreen3", + "darkseagreen4", + "darkslateblue", + "darkslategray", + "darkslategray1", + "darkslategray2", + "darkslategray3", + "darkslategray4", + "darkslategrey", + "darkturquoise", + "darkviolet", + "deeppink", + "deeppink1", + "deeppink2", + "deeppink3", + "deeppink4", + "deepskyblue", + "deepskyblue1", + "deepskyblue2", + "deepskyblue3", + "deepskyblue4", + "dimgray", + "dimgrey", + "dodgerblue", + "dodgerblue1", + "dodgerblue2", + "dodgerblue3", + "dodgerblue4", + "firebrick", + "firebrick1", + "firebrick2", + "firebrick3", + "firebrick4", + "floralwhite", + "forestgreen", + "gainsboro", + "ghostwhite", + "gold", + "gold1", + "gold2", + "gold3", + "gold4", + "goldenrod", + "goldenrod1", + "goldenrod2", + "goldenrod3", + "goldenrod4", + "gray", + "gray0", + "gray1", + "gray2", + "gray3", + "gray4", + "gray5", + "gray6", + "gray7", + "gray8", + "gray9", + "gray10", + "gray11", + "gray12", + "gray13", + "gray14", + "gray15", + "gray16", + "gray17", + "gray18", + "gray19", + "gray20", + "gray21", + "gray22", + "gray23", + "gray24", + "gray25", + "gray26", + "gray27", + "gray28", + "gray29", + "gray30", + "gray31", + "gray32", + "gray33", + "gray34", + "gray35", + "gray36", + "gray37", + "gray38", + "gray39", + "gray40", + "gray41", + "gray42", + "gray43", + "gray44", + "gray45", + "gray46", + "gray47", + "gray48", + "gray49", + "gray50", + "gray51", + "gray52", + "gray53", + "gray54", + "gray55", + "gray56", + "gray57", + "gray58", + "gray59", + "gray60", + "gray61", + "gray62", + "gray63", + "gray64", + "gray65", + "gray66", + "gray67", + "gray68", + "gray69", + "gray70", + "gray71", + "gray72", + "gray73", + "gray74", + "gray75", + "gray76", + "gray77", + "gray78", + "gray79", + "gray80", + "gray81", + "gray82", + "gray83", + "gray84", + "gray85", + "gray86", + "gray87", + "gray88", + "gray89", + "gray90", + "gray91", + "gray92", + "gray93", + "gray94", + "gray95", + "gray96", + "gray97", + "gray98", + "gray99", + "gray100", + "green", + "green1", + "green2", + "green3", + "green4", + "greenyellow", + "grey", + "grey0", + "grey1", + "grey2", + "grey3", + "grey4", + "grey5", + "grey6", + "grey7", + "grey8", + "grey9", + "grey10", + "grey11", + "grey12", + "grey13", + "grey14", + "grey15", + "grey16", + "grey17", + "grey18", + "grey19", + "grey20", + "grey21", + "grey22", + "grey23", + "grey24", + "grey25", + "grey26", + "grey27", + "grey28", + "grey29", + "grey30", + "grey31", + "grey32", + "grey33", + "grey34", + "grey35", + "grey36", + "grey37", + "grey38", + "grey39", + "grey40", + "grey41", + "grey42", + "grey43", + "grey44", + "grey45", + "grey46", + "grey47", + "grey48", + "grey49", + "grey50", + "grey51", + "grey52", + "grey53", + "grey54", + "grey55", + "grey56", + "grey57", + "grey58", + "grey59", + "grey60", + "grey61", + "grey62", + "grey63", + "grey64", + "grey65", + "grey66", + "grey67", + "grey68", + "grey69", + "grey70", + "grey71", + "grey72", + "grey73", + "grey74", + "grey75", + "grey76", + "grey77", + "grey78", + "grey79", + "grey80", + "grey81", + "grey82", + "grey83", + "grey84", + "grey85", + "grey86", + "grey87", + "grey88", + "grey89", + "grey90", + "grey91", + "grey92", + "grey93", + "grey94", + "grey95", + "grey96", + "grey97", + "grey98", + "grey99", + "grey100", + "honeydew", + "honeydew1", + "honeydew2", + "honeydew3", + "honeydew4", + "hotpink", + "hotpink1", + "hotpink2", + "hotpink3", + "hotpink4", + "indianred", + "indianred1", + "indianred2", + "indianred3", + "indianred4", + "ivory", + "ivory1", + "ivory2", + "ivory3", + "ivory4", + "khaki", + "khaki1", + "khaki2", + "khaki3", + "khaki4", + "lavender", + "lavenderblush", + "lavenderblush1", + "lavenderblush2", + "lavenderblush3", + "lavenderblush4", + "lawngreen", + "lemonchiffon", + "lemonchiffon1", + "lemonchiffon2", + "lemonchiffon3", + "lemonchiffon4", + "lightblue", + "lightblue1", + "lightblue2", + "lightblue3", + "lightblue4", + "lightcoral", + "lightcyan", + "lightcyan1", + "lightcyan2", + "lightcyan3", + "lightcyan4", + "lightgoldenrod", + "lightgoldenrod1", + "lightgoldenrod2", + "lightgoldenrod3", + "lightgoldenrod4", + "lightgoldenrodyellow", + "lightgray", + "lightgreen", + "lightgrey", + "lightpink", + "lightpink1", + "lightpink2", + "lightpink3", + "lightpink4", + "lightsalmon", + "lightsalmon1", + "lightsalmon2", + "lightsalmon3", + "lightsalmon4", + "lightseagreen", + "lightskyblue", + "lightskyblue1", + "lightskyblue2", + "lightskyblue3", + "lightskyblue4", + "lightslateblue", + "lightslategray", + "lightslategrey", + "lightsteelblue", + "lightsteelblue1", + "lightsteelblue2", + "lightsteelblue3", + "lightsteelblue4", + "lightyellow", + "lightyellow1", + "lightyellow2", + "lightyellow3", + "lightyellow4", + "limegreen", + "linen", + "magenta", + "magenta1", + "magenta2", + "magenta3", + "magenta4", + "maroon", + "maroon1", + "maroon2", + "maroon3", + "maroon4", + "mediumaquamarine", + "mediumblue", + "mediumorchid", + "mediumorchid1", + "mediumorchid2", + "mediumorchid3", + "mediumorchid4", + "mediumpurple", + "mediumpurple1", + "mediumpurple2", + "mediumpurple3", + "mediumpurple4", + "mediumseagreen", + "mediumslateblue", + "mediumspringgreen", + "mediumturquoise", + "mediumvioletred", + "midnightblue", + "mintcream", + "mistyrose", + "mistyrose1", + "mistyrose2", + "mistyrose3", + "mistyrose4", + "moccasin", + "navajowhite", + "navajowhite1", + "navajowhite2", + "navajowhite3", + "navajowhite4", + "navy", + "navyblue", + "oldlace", + "olivedrab", + "olivedrab1", + "olivedrab2", + "olivedrab3", + "olivedrab4", + "orange", + "orange1", + "orange2", + "orange3", + "orange4", + "orangered", + "orangered1", + "orangered2", + "orangered3", + "orangered4", + "orchid", + "orchid1", + "orchid2", + "orchid3", + "orchid4", + "palegoldenrod", + "palegreen", + "palegreen1", + "palegreen2", + "palegreen3", + "palegreen4", + "paleturquoise", + "paleturquoise1", + "paleturquoise2", + "paleturquoise3", + "paleturquoise4", + "palevioletred", + "palevioletred1", + "palevioletred2", + "palevioletred3", + "palevioletred4", + "papayawhip", + "peachpuff", + "peachpuff1", + "peachpuff2", + "peachpuff3", + "peachpuff4", + "peru", + "pink", + "pink1", + "pink2", + "pink3", + "pink4", + "plum", + "plum1", + "plum2", + "plum3", + "plum4", + "powderblue", + "purple", + "purple1", + "purple2", + "purple3", + "purple4", + "red", + "red1", + "red2", + "red3", + "red4", + "rosybrown", + "rosybrown1", + "rosybrown2", + "rosybrown3", + "rosybrown4", + "royalblue", + "royalblue1", + "royalblue2", + "royalblue3", + "royalblue4", + "saddlebrown", + "salmon", + "salmon1", + "salmon2", + "salmon3", + "salmon4", + "sandybrown", + "seagreen", + "seagreen1", + "seagreen2", + "seagreen3", + "seagreen4", + "seashell", + "seashell1", + "seashell2", + "seashell3", + "seashell4", + "sienna", + "sienna1", + "sienna2", + "sienna3", + "sienna4", + "skyblue", + "skyblue1", + "skyblue2", + "skyblue3", + "skyblue4", + "slateblue", + "slateblue1", + "slateblue2", + "slateblue3", + "slateblue4", + "slategray", + "slategray1", + "slategray2", + "slategray3", + "slategray4", + "slategrey", + "snow", + "snow1", + "snow2", + "snow3", + "snow4", + "springgreen", + "springgreen1", + "springgreen2", + "springgreen3", + "springgreen4", + "steelblue", + "steelblue1", + "steelblue2", + "steelblue3", + "steelblue4", + "tan", + "tan1", + "tan2", + "tan3", + "tan4", + "thistle", + "thistle1", + "thistle2", + "thistle3", + "thistle4", + "tomato", + "tomato1", + "tomato2", + "tomato3", + "tomato4", + "turquoise", + "turquoise1", + "turquoise2", + "turquoise3", + "turquoise4", + "violet", + "violetred", + "violetred1", + "violetred2", + "violetred3", + "violetred4", + "wheat", + "wheat1", + "wheat2", + "wheat3", + "wheat4", + "whitesmoke", + "yellow", + "yellow1", + "yellow2", + "yellow3", + "yellow4", + "yellowgreen" + ], + "defaultValue": ["darkgoldenrod2", "darkolivegreen2", "mediumpurple3", "darkorange2", "lightgreen"], + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "venn_fill_transparency", + "displayName": "Venn Fill Transparency", + "description": "Transparency level for the Venn diagram fill colors. Default: 0.2\n", + "paramType": "STRING", + "paramGroup": "Venn Diagram", + "paramValues": null, + "defaultValue": 0.2, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "venn_border_colors", + "displayName": "Venn Border Colors", + "description": "Colors for the borders of the Venn diagram categories. Default: \"fill colors\" (uses the\nsame colors as `venn_fill_colors`)\n", + "paramType": "SELECT", + "paramGroup": "Venn Diagram", + "paramValues": [ + "black", + "fill colors" + ], + "defaultValue": "fill colors", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "venn_font_size_for_category_names", + "displayName": "Venn Font Size for Category Names", + "description": "Font size for the category names in the Venn diagram. Default: 3\n", + "paramType": "NUMBER", + "paramGroup": "Venn Diagram", + "paramValues": null, + "defaultValue": 3, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "venn_category_names_distance", + "displayName": "Venn Category Names Distance", + "description": "Distance of the category names from the Venn diagram circles. Default: c()\n", + "paramType": "VECTOR", + "paramGroup": "Venn Diagram", + "paramValues": null, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "venn_category_names_position", + "displayName": "Venn Category Names Position", + "description": "Position of the category names in the Venn diagram. Default: c()\n", + "paramType": "VECTOR", + "paramGroup": "Venn Diagram", + "paramValues": null, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "venn_font_size_for_counts", + "displayName": "Venn Font Size for Counts", + "description": "Font size for the counts in the Venn diagram. Default: 6\n", + "paramType": "NUMBER", + "paramGroup": "Venn Diagram", + "paramValues": null, + "defaultValue": 6, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "venn_outer_margin", + "displayName": "Venn Outer Margin", + "description": "Outer margin for the Venn diagram. Default: 0\n", + "paramType": "NUMBER", + "paramGroup": "Venn Diagram", + "paramValues": null, + "defaultValue": 0, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "intersections_order", + "displayName": "Intersections Order", + "description": "Order of the intersections in the plot. Default: \"by size\"\n", + "paramType": "SELECT", + "paramGroup": "Intersection Plot", + "paramValues": [ + "degree", + "freq" + ], + "defaultValue": "degree", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "display_empty_intersections", + "displayName": "Display Empty Intersections", + "description": "If TRUE, displays empty intersections in the plot. Default: FALSE\n", + "paramType": "BOOLEAN", + "paramGroup": "Intersection Plot", + "paramValues": null, + "defaultValue": false, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "intersection_bar_color", + "displayName": "Intersection Bar Color", + "description": "Color for the intersection bars in the plot. Default: \"lightgray\"\n", + "paramType": "SELECT", + "paramGroup": "Intersection Plot", + "paramValues": [ + "steelblue4", + "aquamarine3", + "salmon1", + "lightskyblue3", + "plum3", + "darkolivegreen3", + "goldenrod1", + "burlywood2", + "gray70", + "firebrick2", + "steelblue", + "palegreen4", + "orchid4", + "darkorange1", + "yellow", + "sienna", + "palevioletred1", + "gray60", + "cyan4", + "darkorange3", + "mediumpurple3", + "violetred2", + "olivedrab", + "darkgoldenrod2", + "darkgoldenrod", + "gray40", + "palegreen3", + "thistle3", + "khaki1", + "deeppink2", + "chocolate3", + "paleturquoise3", + "wheat1", + "lightsteelblue", + "salmon", + "sandybrown", + "darkolivegreen2", + "thistle2", + "gray85", + "orchid3", + "darkseagreen1", + "lightgoldenrod1", + "lightskyblue2", + "dodgerblue3", + "darkseagreen3", + "forestgreen", + "lightpink2", + "mediumpurple4", + "lightpink1", + "thistle", + "navajowhite", + "lemonchiffon", + "bisque2", + "mistyrose", + "gray95", + "lightcyan3", + "peachpuff2", + "lightsteelblue2", + "lightyellow2", + "moccasin", + "antiquewhite2", + "gray80", + "lightgrey" + ], + "defaultValue": "steelblue4", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "intersection_line_width", + "displayName": "Intersection Line Width", + "description": "Width of the lines in the intersection plot. Default: 0.5\n", + "paramType": "NUMBER", + "paramGroup": "Intersection Plot", + "paramValues": null, + "defaultValue": 0.7, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "intersection_point_size", + "displayName": "Intersection Point Size", + "description": "Size of the points in the intersection plot. Default: 2\n", + "paramType": "NUMBER", + "paramGroup": "Intersection Plot", + "paramValues": null, + "defaultValue": 2.2, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "table_font_size", + "displayName": "Table Font Size", + "description": "Font size for the table in the plot. Default: 3\n", + "paramType": "NUMBER", + "paramGroup": "Table", + "paramValues": null, + "defaultValue": 0.7, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "table_content", + "displayName": "Table Content", + "description": "Content of the table in the plot. Default: NULL\n", + "paramType": "SELECT", + "paramGroup": "Table", + "paramValues": [ + "all intersections", + "returned intersections" + ], + "defaultValue": "all intersections", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "dpi", + "displayName": "Image Resolution", + "description": "dots-per-inch of the output image (see `ggsave()`) - only used if save_plots is TRUE\n", + "paramType": "NUMBER", + "paramGroup": "Image", + "paramValues": null, + "defaultValue": 300, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "image_height", + "displayName": "Image Height", + "description": "output image height in pixels - only used if save_plots is TRUE\n", + "paramType": "NUMBER", + "paramGroup": "Image", + "paramValues": null, + "defaultValue": 3000, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "image_width", + "displayName": "Image Width", + "description": "output image width in pixels - only used if save_plots is TRUE\n", + "paramType": "NUMBER", + "paramGroup": "Image", + "paramValues": null, + "defaultValue": 4000, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "save_plots", + "displayName": "Save Plots", + "description": "Whether to save plots to files during analysis (Defaults to `TRUE`, overwritable using option 'moo_save_plots' or environment variable 'MOO_SAVE_PLOTS')\n", + "paramType": "BOOLEAN", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "outputs": { + "DataFrame": { + "type": "file", + "name": "venn_diagram_dataframe.rds" + }, + "figures": { + "type": "file", + "name": "figures/diff/venn_diagram.png" + } + } +} diff --git a/code/MOSuite/inst/extdata/galaxy/2_blueprints/plot_volcano_enhanced.json b/code/MOSuite/inst/extdata/galaxy/2_blueprints/plot_volcano_enhanced.json new file mode 100644 index 0000000..b9acb91 --- /dev/null +++ b/code/MOSuite/inst/extdata/galaxy/2_blueprints/plot_volcano_enhanced.json @@ -0,0 +1,329 @@ +{ + "r_function": "plot_volcano_enhanced", + "title": "Plot Volcano - Enhanced\n", + "description": "Uses \nlist(list(\"https://bioconductor.org/packages/release/bioc/html/EnhancedVolcano.html\"), list(\"Bioconductor's Enhanced Volcano Plot\"))\n.\nAn S7 generic with methods for \nlist(\"multiOmicDataSet\")\n and \nlist(\"data.frame\")\n.\n", + "columns": [ + { + "key": "feature_id_colname", + "displayName": "Column with Feature ID", + "description": "The column from the counts data containing the Feature IDs (Usually Gene or Protein ID).\nThis is usually the first column of your input Counts Matrix. Only columns of Text type from your input Counts\nMatrix will be available to select for this parameter. (Default: `NULL` - first column in the counts matrix will be\nused.)\n", + "paramGroup": "Basic", + "sourceDataset": "DEG_Table", + "columnType": "STRING", + "isMulti": null + }, + { + "key": "signif_colname", + "displayName": "Significance Column", + "description": "column name of significance values (e.g., adjusted p-values or FDR). This column will be used\nto determine which points are considered significant in the volcano plot.\n", + "paramGroup": "Basic", + "sourceDataset": "DEG_Table", + "defaultValue": ["B-A_adjpval", "B-C_adjpval"], + "columnType": "NUMBER", + "isMulti": true + }, + { + "key": "change_colname", + "displayName": "Log2 Fold Change Column", + "description": "column name of fold change values.\n", + "paramGroup": "Basic", + "sourceDataset": "DEG_Table", + "defaultValue": ["B-A_logFC", "B-C_logFC"], + "columnType": "NUMBER", + "isMulti": true + } + ], + "inputDatasets": [ + { + "key": "moo_input_rds", + "displayName": "MOO input Rds", + "description": "File path to read the input multiOmicDataSet object (MOO)", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "parameters": [ + { + "key": "moo_output_rds", + "displayName": "Summary dataframe output Rds", + "description": "File path to the summary dataframe as an Rds file", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "enhanced_volcano_plot.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "signif_threshold", + "displayName": "P-Value Threshold", + "description": "Numeric value specifying the significance cutoff for p-values (i.e. filters on\n`signif_colname`)\n", + "paramType": "NUMBER", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": 0.05, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "change_threshold", + "displayName": "Log2 Fold Change Threshold", + "description": "Numeric value specifying the fold change cutoff for significance (i.e. filters on\n`change_colname`)\n", + "paramType": "NUMBER", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": 1, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "value_to_sort_the_output_dataset", + "displayName": "How to sort the output dataset", + "description": "How to sort the output dataset. Options are \"fold-change\" or \"p-value\".\n", + "paramType": "SELECT", + "paramGroup": "Label", + "paramValues": [ + "p-value", + "fold-change" + ], + "defaultValue": "p-value", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "num_features_to_label", + "displayName": "Number of Features to Label", + "description": "Number of top features/genes to label in the volcano plot. Default is 30.\n", + "paramType": "NUMBER", + "paramGroup": "Label", + "paramValues": null, + "defaultValue": 30, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "use_only_addition_labels", + "displayName": "Label Only My Feature List", + "description": "If `TRUE`, only the additional labels specified in `additional_labels` will be used\nfor labeling in the volcano plot, ignoring the top features.\n", + "paramType": "BOOLEAN", + "paramGroup": "Label", + "paramValues": null, + "defaultValue": false, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "additional_labels", + "displayName": "My Feature List", + "description": "comma-separated string of feature names or IDs to include in the volcano plot.\n", + "paramType": "STRING", + "paramGroup": "Label", + "paramValues": null, + "defaultValue": "", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "lab_size", + "displayName": "Label Size", + "description": "Size of the labels in the volcano plot.\n", + "paramType": "NUMBER", + "paramGroup": "Label", + "paramValues": null, + "defaultValue": 4, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "change_sig_name", + "displayName": "Custom Significance Label", + "description": "Name for the significance column in the plot. Default is \"p-value\".\n", + "paramType": "STRING", + "paramGroup": "Title and Axis labels", + "paramValues": null, + "defaultValue": "p-value", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "change_lfc_name", + "displayName": "Custom Log Fold Change Label", + "description": "Name for the fold change column in the plot. Default is \"log2FC\".\n", + "paramType": "STRING", + "paramGroup": "Title and Axis labels", + "paramValues": null, + "defaultValue": "log2FC", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "use_custom_lab", + "displayName": "Use Custom Labels", + "description": "If TRUE, uses custom labels for the plot (set by `change_sig_name` and `change_lfc_name`)\n", + "paramType": "BOOLEAN", + "paramGroup": "Title and Axis Labels", + "paramValues": null, + "defaultValue": false, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "title", + "displayName": "Plot Title", + "description": "Title of the plot. Default is \"Volcano Plots\".\n", + "paramType": "STRING", + "paramGroup": "Title and Axis labels", + "paramValues": null, + "defaultValue": "Volcano Plots", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "ylim", + "displayName": "Y-Limit", + "description": "Y-axis limits for the plot.\n", + "paramType": "NUMBER", + "paramGroup": "Plot", + "paramValues": null, + "defaultValue": 0, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "custom_xlim", + "displayName": "Custom X-axis limits", + "description": "Custom X-axis limits for the plot.\n", + "paramType": "STRING", + "paramGroup": "Plot", + "paramValues": null, + "defaultValue": "", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "xlim_additional", + "displayName": "X-Limit Padding", + "description": "Additional space to add to the X-axis limits.\n", + "paramType": "NUMBER", + "paramGroup": "Plot", + "paramValues": null, + "defaultValue": 0, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "ylim_additional", + "displayName": "Y-Limit Padding", + "description": "Additional space to add to the Y-axis limits.\n", + "paramType": "NUMBER", + "paramGroup": "Plot", + "paramValues": null, + "defaultValue": 0, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "axis_lab_size", + "displayName": "Axis Label Size", + "description": "Size of the axis labels.\n", + "paramType": "NUMBER", + "paramGroup": "Plot", + "paramValues": null, + "defaultValue": 24, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "point_size", + "displayName": "Point Size", + "description": "Size of the points in the plot.\n", + "paramType": "NUMBER", + "paramGroup": "Plot", + "paramValues": null, + "defaultValue": 2, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "image_width", + "displayName": "Image Width", + "description": "output image width in pixels - only used if save_plots is TRUE\n", + "paramType": "NUMBER", + "paramGroup": "Image", + "paramValues": null, + "defaultValue": 3000, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "image_height", + "displayName": "Image Height", + "description": "output image height in pixels - only used if save_plots is TRUE\n", + "paramType": "NUMBER", + "paramGroup": "Image", + "paramValues": null, + "defaultValue": 3000, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "dpi", + "displayName": "Image Resolution (DPI)", + "description": "dots-per-inch of the output image (see `ggsave()`) - only used if save_plots is TRUE\n", + "paramType": "NUMBER", + "paramGroup": "Image", + "paramValues": null, + "defaultValue": 300, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "save_plots", + "displayName": "Save Plots", + "description": "Whether to save plots to files during analysis (Defaults to `TRUE`, overwritable using option 'moo_save_plots' or environment variable 'MOO_SAVE_PLOTS')\n", + "paramType": "BOOLEAN", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "outputs": { + "DataFrame": { + "type": "file", + "name": "enhanced_volcano_dataframe.rds" + }, + "figures": { + "type": "file", + "name": "figures/diff/volcano_enhanced.png" + } + } +} diff --git a/code/MOSuite/inst/extdata/galaxy/2_blueprints/plot_volcano_summary.json b/code/MOSuite/inst/extdata/galaxy/2_blueprints/plot_volcano_summary.json new file mode 100644 index 0000000..9e3cf80 --- /dev/null +++ b/code/MOSuite/inst/extdata/galaxy/2_blueprints/plot_volcano_summary.json @@ -0,0 +1,5129 @@ +{ + "r_function": "plot_volcano_summary", + "title": "Plot Volcano - Summary\n", + "description": "Produces one volcano plot for each tested contrast in the input DEG table.\nIt can be sorted by either fold change, t-statistic, or p-value. The returned dataset includes one row for each\nsignificant gene in each contrast, and contains columns from the DEG analysis of that contrast as well as columns\nuseful to the Venn diagram template downstream.\nAn S7 generic with methods for \nlist(\"multiOmicDataSet\")\n and \nlist(\"data.frame\")\n.\n", + "columns": [ + { + "key": "feature_id_colname", + "displayName": "Gene Names Column", + "description": "The column from the counts data containing the Feature IDs (Usually Gene or Protein ID).\nThis is usually the first column of your input Counts Matrix. Only columns of Text type from your input Counts\nMatrix will be available to select for this parameter. (Default: `NULL` - first column in the counts matrix will be\nused.)\n", + "paramGroup": "Basic", + "sourceDataset": "DEG_Table", + "columnType": "STRING", + "isMulti": null + } + ], + "inputDatasets": [ + { + "key": "moo_input_rds", + "displayName": "MOO input Rds", + "description": "File path to read the input multiOmicDataSet object (MOO)", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "parameters": [ + { + "key": "moo_output_rds", + "displayName": "Summary dataframe output Rds", + "description": "File path to output summary data as an Rds file", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "signif_colname", + "displayName": "Significance column name", + "description": "column name of significance values (e.g., adjusted p-values or FDR). This column will be used\nto determine which points are considered significant in the volcano plot.\n", + "paramType": "SELECT", + "paramGroup": "Basic", + "paramValues": [ + "pval", + "adjpval" + ], + "defaultValue": "pval", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "signif_threshold", + "displayName": "P-Value Threshold", + "description": "Numeric value specifying the significance cutoff for p-values (i.e. filters on\n`signif_colname`)\n", + "paramType": "NUMBER", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": 0.05, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "change_threshold", + "displayName": "Log2 Fold Change Threshold", + "description": "Numeric value specifying the fold change cutoff for significance (i.e. filters on\n`change_colname`)\n", + "paramType": "NUMBER", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": 1, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "value_to_sort_the_output_dataset", + "displayName": "Choose How to sort the output dataset", + "description": "How to sort the output dataset. Options are \"fold-change\" or \"p-value\".\n", + "paramType": "SELECT", + "paramGroup": "Gene Name Label", + "paramValues": [ + "fold-change", + "p-value", + "t-statistic" + ], + "defaultValue": "t-statistic", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "num_features_to_label", + "displayName": "Number of Genes to Label", + "description": "Number of top features/genes to label in the volcano plot. Default is 30.\n", + "paramType": "NUMBER", + "paramGroup": "Gene Name Label", + "paramValues": null, + "defaultValue": 30, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "add_features", + "displayName": "Add Custom Features List To Labels", + "description": "Add custom_gene_list To Labels. Set TRUE when you want to label a specific set of features\n(features) in the \"custom_gene_list\" parameter\" IN ADDITION to the number of features you set in the \"Number of\nFeatures to Label\" parameter.\n", + "paramType": "BOOLEAN", + "paramGroup": "Gene Name Label", + "paramValues": null, + "defaultValue": false, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "label_features", + "displayName": "Label Only Custom Features List", + "description": "Select TRUE when you want to label ONLY a specific list of features(features) given in the\n\"custom_gene_list\" parameter.\n", + "paramType": "BOOLEAN", + "paramGroup": "Gene Name Label", + "paramValues": null, + "defaultValue": false, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "custom_gene_list", + "displayName": "Custom Feature/Gene List", + "description": "Provide a list of features (comma separated) to be labeled on the volcano plot. You must\ntoggle one of the following ON to see these labels: \"Add features\" or \"Label Only My Feature List\".\n", + "paramType": "STRING", + "paramGroup": "Gene Name Label", + "paramValues": null, + "defaultValue": "", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "default_label_color", + "displayName": "Default Feature Label Text Color", + "description": "Set the color for the text used to add feature (gene) name labels to points.\n", + "paramType": "SELECT", + "paramGroup": "Gene Name Label", + "paramValues": [ + "white", + "aliceblue", + "antiquewhite", + "antiquewhite1", + "antiquewhite2", + "antiquewhite3", + "antiquewhite4", + "aquamarine", + "aquamarine1", + "aquamarine2", + "aquamarine3", + "aquamarine4", + "azure", + "azure1", + "azure2", + "azure3", + "azure4", + "beige", + "bisque", + "bisque1", + "bisque2", + "bisque3", + "bisque4", + "black", + "blanchedalmond", + "blue", + "blue1", + "blue2", + "blue3", + "blue4", + "blueviolet", + "brown", + "brown1", + "brown2", + "brown3", + "brown4", + "burlywood", + "burlywood1", + "burlywood2", + "burlywood3", + "burlywood4", + "cadetblue", + "cadetblue1", + "cadetblue2", + "cadetblue3", + "cadetblue4", + "chartreuse", + "chartreuse1", + "chartreuse2", + "chartreuse3", + "chartreuse4", + "chocolate", + "chocolate1", + "chocolate2", + "chocolate3", + "chocolate4", + "coral", + "coral1", + "coral2", + "coral3", + "coral4", + "cornflowerblue", + "cornsilk", + "cornsilk1", + "cornsilk2", + "cornsilk3", + "cornsilk4", + "cyan", + "cyan1", + "cyan2", + "cyan3", + "cyan4", + "darkblue", + "darkcyan", + "darkgoldenrod", + "darkgoldenrod1", + "darkgoldenrod2", + "darkgoldenrod3", + "darkgoldenrod4", + "darkgray", + "darkgreen", + "darkgrey", + "darkkhaki", + "darkmagenta", + "darkolivegreen", + "darkolivegreen1", + "darkolivegreen2", + "darkolivegreen3", + "darkolivegreen4", + "darkorange", + "darkorange1", + "darkorange2", + "darkorange3", + "darkorange4", + "darkorchid", + "darkorchid1", + "darkorchid2", + "darkorchid3", + "darkorchid4", + "darkred", + "darksalmon", + "darkseagreen", + "darkseagreen1", + "darkseagreen2", + "darkseagreen3", + "darkseagreen4", + "darkslateblue", + "darkslategray", + "darkslategray1", + "darkslategray2", + "darkslategray3", + "darkslategray4", + "darkslategrey", + "darkturquoise", + "darkviolet", + "deeppink", + "deeppink1", + "deeppink2", + "deeppink3", + "deeppink4", + "deepskyblue", + "deepskyblue1", + "deepskyblue2", + "deepskyblue3", + "deepskyblue4", + "dimgray", + "dimgrey", + "dodgerblue", + "dodgerblue1", + "dodgerblue2", + "dodgerblue3", + "dodgerblue4", + "firebrick", + "firebrick1", + "firebrick2", + "firebrick3", + "firebrick4", + "floralwhite", + "forestgreen", + "gainsboro", + "ghostwhite", + "gold", + "gold1", + "gold2", + "gold3", + "gold4", + "goldenrod", + "goldenrod1", + "goldenrod2", + "goldenrod3", + "goldenrod4", + "gray", + "gray0", + "gray1", + "gray2", + "gray3", + "gray4", + "gray5", + "gray6", + "gray7", + "gray8", + "gray9", + "gray10", + "gray11", + "gray12", + "gray13", + "gray14", + "gray15", + "gray16", + "gray17", + "gray18", + "gray19", + "gray20", + "gray21", + "gray22", + "gray23", + "gray24", + "gray25", + "gray26", + "gray27", + "gray28", + "gray29", + "gray30", + "gray31", + "gray32", + "gray33", + "gray34", + "gray35", + "gray36", + "gray37", + "gray38", + "gray39", + "gray40", + "gray41", + "gray42", + "gray43", + "gray44", + "gray45", + "gray46", + "gray47", + "gray48", + "gray49", + "gray50", + "gray51", + "gray52", + "gray53", + "gray54", + "gray55", + "gray56", + "gray57", + "gray58", + "gray59", + "gray60", + "gray61", + "gray62", + "gray63", + "gray64", + "gray65", + "gray66", + "gray67", + "gray68", + "gray69", + "gray70", + "gray71", + "gray72", + "gray73", + "gray74", + "gray75", + "gray76", + "gray77", + "gray78", + "gray79", + "gray80", + "gray81", + "gray82", + "gray83", + "gray84", + "gray85", + "gray86", + "gray87", + "gray88", + "gray89", + "gray90", + "gray91", + "gray92", + "gray93", + "gray94", + "gray95", + "gray96", + "gray97", + "gray98", + "gray99", + "gray100", + "green", + "green1", + "green2", + "green3", + "green4", + "greenyellow", + "grey", + "grey0", + "grey1", + "grey2", + "grey3", + "grey4", + "grey5", + "grey6", + "grey7", + "grey8", + "grey9", + "grey10", + "grey11", + "grey12", + "grey13", + "grey14", + "grey15", + "grey16", + "grey17", + "grey18", + "grey19", + "grey20", + "grey21", + "grey22", + "grey23", + "grey24", + "grey25", + "grey26", + "grey27", + "grey28", + "grey29", + "grey30", + "grey31", + "grey32", + "grey33", + "grey34", + "grey35", + "grey36", + "grey37", + "grey38", + "grey39", + "grey40", + "grey41", + "grey42", + "grey43", + "grey44", + "grey45", + "grey46", + "grey47", + "grey48", + "grey49", + "grey50", + "grey51", + "grey52", + "grey53", + "grey54", + "grey55", + "grey56", + "grey57", + "grey58", + "grey59", + "grey60", + "grey61", + "grey62", + "grey63", + "grey64", + "grey65", + "grey66", + "grey67", + "grey68", + "grey69", + "grey70", + "grey71", + "grey72", + "grey73", + "grey74", + "grey75", + "grey76", + "grey77", + "grey78", + "grey79", + "grey80", + "grey81", + "grey82", + "grey83", + "grey84", + "grey85", + "grey86", + "grey87", + "grey88", + "grey89", + "grey90", + "grey91", + "grey92", + "grey93", + "grey94", + "grey95", + "grey96", + "grey97", + "grey98", + "grey99", + "grey100", + "honeydew", + "honeydew1", + "honeydew2", + "honeydew3", + "honeydew4", + "hotpink", + "hotpink1", + "hotpink2", + "hotpink3", + "hotpink4", + "indianred", + "indianred1", + "indianred2", + "indianred3", + "indianred4", + "ivory", + "ivory1", + "ivory2", + "ivory3", + "ivory4", + "khaki", + "khaki1", + "khaki2", + "khaki3", + "khaki4", + "lavender", + "lavenderblush", + "lavenderblush1", + "lavenderblush2", + "lavenderblush3", + "lavenderblush4", + "lawngreen", + "lemonchiffon", + "lemonchiffon1", + "lemonchiffon2", + "lemonchiffon3", + "lemonchiffon4", + "lightblue", + "lightblue1", + "lightblue2", + "lightblue3", + "lightblue4", + "lightcoral", + "lightcyan", + "lightcyan1", + "lightcyan2", + "lightcyan3", + "lightcyan4", + "lightgoldenrod", + "lightgoldenrod1", + "lightgoldenrod2", + "lightgoldenrod3", + "lightgoldenrod4", + "lightgoldenrodyellow", + "lightgray", + "lightgreen", + "lightgrey", + "lightpink", + "lightpink1", + "lightpink2", + "lightpink3", + "lightpink4", + "lightsalmon", + "lightsalmon1", + "lightsalmon2", + "lightsalmon3", + "lightsalmon4", + "lightseagreen", + "lightskyblue", + "lightskyblue1", + "lightskyblue2", + "lightskyblue3", + "lightskyblue4", + "lightslateblue", + "lightslategray", + "lightslategrey", + "lightsteelblue", + "lightsteelblue1", + "lightsteelblue2", + "lightsteelblue3", + "lightsteelblue4", + "lightyellow", + "lightyellow1", + "lightyellow2", + "lightyellow3", + "lightyellow4", + "limegreen", + "linen", + "magenta", + "magenta1", + "magenta2", + "magenta3", + "magenta4", + "maroon", + "maroon1", + "maroon2", + "maroon3", + "maroon4", + "mediumaquamarine", + "mediumblue", + "mediumorchid", + "mediumorchid1", + "mediumorchid2", + "mediumorchid3", + "mediumorchid4", + "mediumpurple", + "mediumpurple1", + "mediumpurple2", + "mediumpurple3", + "mediumpurple4", + "mediumseagreen", + "mediumslateblue", + "mediumspringgreen", + "mediumturquoise", + "mediumvioletred", + "midnightblue", + "mintcream", + "mistyrose", + "mistyrose1", + "mistyrose2", + "mistyrose3", + "mistyrose4", + "moccasin", + "navajowhite", + "navajowhite1", + "navajowhite2", + "navajowhite3", + "navajowhite4", + "navy", + "navyblue", + "oldlace", + "olivedrab", + "olivedrab1", + "olivedrab2", + "olivedrab3", + "olivedrab4", + "orange", + "orange1", + "orange2", + "orange3", + "orange4", + "orangered", + "orangered1", + "orangered2", + "orangered3", + "orangered4", + "orchid", + "orchid1", + "orchid2", + "orchid3", + "orchid4", + "palegoldenrod", + "palegreen", + "palegreen1", + "palegreen2", + "palegreen3", + "palegreen4", + "paleturquoise", + "paleturquoise1", + "paleturquoise2", + "paleturquoise3", + "paleturquoise4", + "palevioletred", + "palevioletred1", + "palevioletred2", + "palevioletred3", + "palevioletred4", + "papayawhip", + "peachpuff", + "peachpuff1", + "peachpuff2", + "peachpuff3", + "peachpuff4", + "peru", + "pink", + "pink1", + "pink2", + "pink3", + "pink4", + "plum", + "plum1", + "plum2", + "plum3", + "plum4", + "powderblue", + "purple", + "purple1", + "purple2", + "purple3", + "purple4", + "red", + "red1", + "red2", + "red3", + "red4", + "rosybrown", + "rosybrown1", + "rosybrown2", + "rosybrown3", + "rosybrown4", + "royalblue", + "royalblue1", + "royalblue2", + "royalblue3", + "royalblue4", + "saddlebrown", + "salmon", + "salmon1", + "salmon2", + "salmon3", + "salmon4", + "sandybrown", + "seagreen", + "seagreen1", + "seagreen2", + "seagreen3", + "seagreen4", + "seashell", + "seashell1", + "seashell2", + "seashell3", + "seashell4", + "sienna", + "sienna1", + "sienna2", + "sienna3", + "sienna4", + "skyblue", + "skyblue1", + "skyblue2", + "skyblue3", + "skyblue4", + "slateblue", + "slateblue1", + "slateblue2", + "slateblue3", + "slateblue4", + "slategray", + "slategray1", + "slategray2", + "slategray3", + "slategray4", + "slategrey", + "snow", + "snow1", + "snow2", + "snow3", + "snow4", + "springgreen", + "springgreen1", + "springgreen2", + "springgreen3", + "springgreen4", + "steelblue", + "steelblue1", + "steelblue2", + "steelblue3", + "steelblue4", + "tan", + "tan1", + "tan2", + "tan3", + "tan4", + "thistle", + "thistle1", + "thistle2", + "thistle3", + "thistle4", + "tomato", + "tomato1", + "tomato2", + "tomato3", + "tomato4", + "turquoise", + "turquoise1", + "turquoise2", + "turquoise3", + "turquoise4", + "violet", + "violetred", + "violetred1", + "violetred2", + "violetred3", + "violetred4", + "wheat", + "wheat1", + "wheat2", + "wheat3", + "wheat4", + "whitesmoke", + "yellow", + "yellow1", + "yellow2", + "yellow3", + "yellow4", + "yellowgreen" + ], + "defaultValue": "black", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "custom_label_color", + "displayName": "Feature Label Text Color for custom features list", + "description": "Set the color for the specific list of features (features) provided in the \"Feature List\"\nparameter.\n", + "paramType": "SELECT", + "paramGroup": "Gene Name Label", + "paramValues": [ + "white", + "aliceblue", + "antiquewhite", + "antiquewhite1", + "antiquewhite2", + "antiquewhite3", + "antiquewhite4", + "aquamarine", + "aquamarine1", + "aquamarine2", + "aquamarine3", + "aquamarine4", + "azure", + "azure1", + "azure2", + "azure3", + "azure4", + "beige", + "bisque", + "bisque1", + "bisque2", + "bisque3", + "bisque4", + "black", + "blanchedalmond", + "blue", + "blue1", + "blue2", + "blue3", + "blue4", + "blueviolet", + "brown", + "brown1", + "brown2", + "brown3", + "brown4", + "burlywood", + "burlywood1", + "burlywood2", + "burlywood3", + "burlywood4", + "cadetblue", + "cadetblue1", + "cadetblue2", + "cadetblue3", + "cadetblue4", + "chartreuse", + "chartreuse1", + "chartreuse2", + "chartreuse3", + "chartreuse4", + "chocolate", + "chocolate1", + "chocolate2", + "chocolate3", + "chocolate4", + "coral", + "coral1", + "coral2", + "coral3", + "coral4", + "cornflowerblue", + "cornsilk", + "cornsilk1", + "cornsilk2", + "cornsilk3", + "cornsilk4", + "cyan", + "cyan1", + "cyan2", + "cyan3", + "cyan4", + "darkblue", + "darkcyan", + "darkgoldenrod", + "darkgoldenrod1", + "darkgoldenrod2", + "darkgoldenrod3", + "darkgoldenrod4", + "darkgray", + "darkgreen", + "darkgrey", + "darkkhaki", + "darkmagenta", + "darkolivegreen", + "darkolivegreen1", + "darkolivegreen2", + "darkolivegreen3", + "darkolivegreen4", + "darkorange", + "darkorange1", + "darkorange2", + "darkorange3", + "darkorange4", + "darkorchid", + "darkorchid1", + "darkorchid2", + "darkorchid3", + "darkorchid4", + "darkred", + "darksalmon", + "darkseagreen", + "darkseagreen1", + "darkseagreen2", + "darkseagreen3", + "darkseagreen4", + "darkslateblue", + "darkslategray", + "darkslategray1", + "darkslategray2", + "darkslategray3", + "darkslategray4", + "darkslategrey", + "darkturquoise", + "darkviolet", + "deeppink", + "deeppink1", + "deeppink2", + "deeppink3", + "deeppink4", + "deepskyblue", + "deepskyblue1", + "deepskyblue2", + "deepskyblue3", + "deepskyblue4", + "dimgray", + "dimgrey", + "dodgerblue", + "dodgerblue1", + "dodgerblue2", + "dodgerblue3", + "dodgerblue4", + "firebrick", + "firebrick1", + "firebrick2", + "firebrick3", + "firebrick4", + "floralwhite", + "forestgreen", + "gainsboro", + "ghostwhite", + "gold", + "gold1", + "gold2", + "gold3", + "gold4", + "goldenrod", + "goldenrod1", + "goldenrod2", + "goldenrod3", + "goldenrod4", + "gray", + "gray0", + "gray1", + "gray2", + "gray3", + "gray4", + "gray5", + "gray6", + "gray7", + "gray8", + "gray9", + "gray10", + "gray11", + "gray12", + "gray13", + "gray14", + "gray15", + "gray16", + "gray17", + "gray18", + "gray19", + "gray20", + "gray21", + "gray22", + "gray23", + "gray24", + "gray25", + "gray26", + "gray27", + "gray28", + "gray29", + "gray30", + "gray31", + "gray32", + "gray33", + "gray34", + "gray35", + "gray36", + "gray37", + "gray38", + "gray39", + "gray40", + "gray41", + "gray42", + "gray43", + "gray44", + "gray45", + "gray46", + "gray47", + "gray48", + "gray49", + "gray50", + "gray51", + "gray52", + "gray53", + "gray54", + "gray55", + "gray56", + "gray57", + "gray58", + "gray59", + "gray60", + "gray61", + "gray62", + "gray63", + "gray64", + "gray65", + "gray66", + "gray67", + "gray68", + "gray69", + "gray70", + "gray71", + "gray72", + "gray73", + "gray74", + "gray75", + "gray76", + "gray77", + "gray78", + "gray79", + "gray80", + "gray81", + "gray82", + "gray83", + "gray84", + "gray85", + "gray86", + "gray87", + "gray88", + "gray89", + "gray90", + "gray91", + "gray92", + "gray93", + "gray94", + "gray95", + "gray96", + "gray97", + "gray98", + "gray99", + "gray100", + "green", + "green1", + "green2", + "green3", + "green4", + "greenyellow", + "grey", + "grey0", + "grey1", + "grey2", + "grey3", + "grey4", + "grey5", + "grey6", + "grey7", + "grey8", + "grey9", + "grey10", + "grey11", + "grey12", + "grey13", + "grey14", + "grey15", + "grey16", + "grey17", + "grey18", + "grey19", + "grey20", + "grey21", + "grey22", + "grey23", + "grey24", + "grey25", + "grey26", + "grey27", + "grey28", + "grey29", + "grey30", + "grey31", + "grey32", + "grey33", + "grey34", + "grey35", + "grey36", + "grey37", + "grey38", + "grey39", + "grey40", + "grey41", + "grey42", + "grey43", + "grey44", + "grey45", + "grey46", + "grey47", + "grey48", + "grey49", + "grey50", + "grey51", + "grey52", + "grey53", + "grey54", + "grey55", + "grey56", + "grey57", + "grey58", + "grey59", + "grey60", + "grey61", + "grey62", + "grey63", + "grey64", + "grey65", + "grey66", + "grey67", + "grey68", + "grey69", + "grey70", + "grey71", + "grey72", + "grey73", + "grey74", + "grey75", + "grey76", + "grey77", + "grey78", + "grey79", + "grey80", + "grey81", + "grey82", + "grey83", + "grey84", + "grey85", + "grey86", + "grey87", + "grey88", + "grey89", + "grey90", + "grey91", + "grey92", + "grey93", + "grey94", + "grey95", + "grey96", + "grey97", + "grey98", + "grey99", + "grey100", + "honeydew", + "honeydew1", + "honeydew2", + "honeydew3", + "honeydew4", + "hotpink", + "hotpink1", + "hotpink2", + "hotpink3", + "hotpink4", + "indianred", + "indianred1", + "indianred2", + "indianred3", + "indianred4", + "ivory", + "ivory1", + "ivory2", + "ivory3", + "ivory4", + "khaki", + "khaki1", + "khaki2", + "khaki3", + "khaki4", + "lavender", + "lavenderblush", + "lavenderblush1", + "lavenderblush2", + "lavenderblush3", + "lavenderblush4", + "lawngreen", + "lemonchiffon", + "lemonchiffon1", + "lemonchiffon2", + "lemonchiffon3", + "lemonchiffon4", + "lightblue", + "lightblue1", + "lightblue2", + "lightblue3", + "lightblue4", + "lightcoral", + "lightcyan", + "lightcyan1", + "lightcyan2", + "lightcyan3", + "lightcyan4", + "lightgoldenrod", + "lightgoldenrod1", + "lightgoldenrod2", + "lightgoldenrod3", + "lightgoldenrod4", + "lightgoldenrodyellow", + "lightgray", + "lightgreen", + "lightgrey", + "lightpink", + "lightpink1", + "lightpink2", + "lightpink3", + "lightpink4", + "lightsalmon", + "lightsalmon1", + "lightsalmon2", + "lightsalmon3", + "lightsalmon4", + "lightseagreen", + "lightskyblue", + "lightskyblue1", + "lightskyblue2", + "lightskyblue3", + "lightskyblue4", + "lightslateblue", + "lightslategray", + "lightslategrey", + "lightsteelblue", + "lightsteelblue1", + "lightsteelblue2", + "lightsteelblue3", + "lightsteelblue4", + "lightyellow", + "lightyellow1", + "lightyellow2", + "lightyellow3", + "lightyellow4", + "limegreen", + "linen", + "magenta", + "magenta1", + "magenta2", + "magenta3", + "magenta4", + "maroon", + "maroon1", + "maroon2", + "maroon3", + "maroon4", + "mediumaquamarine", + "mediumblue", + "mediumorchid", + "mediumorchid1", + "mediumorchid2", + "mediumorchid3", + "mediumorchid4", + "mediumpurple", + "mediumpurple1", + "mediumpurple2", + "mediumpurple3", + "mediumpurple4", + "mediumseagreen", + "mediumslateblue", + "mediumspringgreen", + "mediumturquoise", + "mediumvioletred", + "midnightblue", + "mintcream", + "mistyrose", + "mistyrose1", + "mistyrose2", + "mistyrose3", + "mistyrose4", + "moccasin", + "navajowhite", + "navajowhite1", + "navajowhite2", + "navajowhite3", + "navajowhite4", + "navy", + "navyblue", + "oldlace", + "olivedrab", + "olivedrab1", + "olivedrab2", + "olivedrab3", + "olivedrab4", + "orange", + "orange1", + "orange2", + "orange3", + "orange4", + "orangered", + "orangered1", + "orangered2", + "orangered3", + "orangered4", + "orchid", + "orchid1", + "orchid2", + "orchid3", + "orchid4", + "palegoldenrod", + "palegreen", + "palegreen1", + "palegreen2", + "palegreen3", + "palegreen4", + "paleturquoise", + "paleturquoise1", + "paleturquoise2", + "paleturquoise3", + "paleturquoise4", + "palevioletred", + "palevioletred1", + "palevioletred2", + "palevioletred3", + "palevioletred4", + "papayawhip", + "peachpuff", + "peachpuff1", + "peachpuff2", + "peachpuff3", + "peachpuff4", + "peru", + "pink", + "pink1", + "pink2", + "pink3", + "pink4", + "plum", + "plum1", + "plum2", + "plum3", + "plum4", + "powderblue", + "purple", + "purple1", + "purple2", + "purple3", + "purple4", + "red", + "red1", + "red2", + "red3", + "red4", + "rosybrown", + "rosybrown1", + "rosybrown2", + "rosybrown3", + "rosybrown4", + "royalblue", + "royalblue1", + "royalblue2", + "royalblue3", + "royalblue4", + "saddlebrown", + "salmon", + "salmon1", + "salmon2", + "salmon3", + "salmon4", + "sandybrown", + "seagreen", + "seagreen1", + "seagreen2", + "seagreen3", + "seagreen4", + "seashell", + "seashell1", + "seashell2", + "seashell3", + "seashell4", + "sienna", + "sienna1", + "sienna2", + "sienna3", + "sienna4", + "skyblue", + "skyblue1", + "skyblue2", + "skyblue3", + "skyblue4", + "slateblue", + "slateblue1", + "slateblue2", + "slateblue3", + "slateblue4", + "slategray", + "slategray1", + "slategray2", + "slategray3", + "slategray4", + "slategrey", + "snow", + "snow1", + "snow2", + "snow3", + "snow4", + "springgreen", + "springgreen1", + "springgreen2", + "springgreen3", + "springgreen4", + "steelblue", + "steelblue1", + "steelblue2", + "steelblue3", + "steelblue4", + "tan", + "tan1", + "tan2", + "tan3", + "tan4", + "thistle", + "thistle1", + "thistle2", + "thistle3", + "thistle4", + "tomato", + "tomato1", + "tomato2", + "tomato3", + "tomato4", + "turquoise", + "turquoise1", + "turquoise2", + "turquoise3", + "turquoise4", + "violet", + "violetred", + "violetred1", + "violetred2", + "violetred3", + "violetred4", + "wheat", + "wheat1", + "wheat2", + "wheat3", + "wheat4", + "whitesmoke", + "yellow", + "yellow1", + "yellow2", + "yellow3", + "yellow4", + "yellowgreen" + ], + "defaultValue": "green3", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "label_x_adj", + "displayName": "Label Position Adjustment (X-Axis)", + "description": "adjust position of the labels on the x-axis. Default: 0.2\n", + "paramType": "NUMBER", + "paramGroup": "Gene Name Label", + "paramValues": null, + "defaultValue": 0.2, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "label_y_adj", + "displayName": "Label Position Adjustment (Y-Axis)", + "description": "adjust position of the labels on the y-axis. Default: 0.2\n", + "paramType": "NUMBER", + "paramGroup": "Gene Name Label", + "paramValues": null, + "defaultValue": 0.2, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "line_thickness", + "displayName": "Line Segment Thickness", + "description": "Set the thickness of the lines in the plot. Default: 0.5\n", + "paramType": "NUMBER", + "paramGroup": "Gene Name Label", + "paramValues": null, + "defaultValue": 0.5, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "label_font_size", + "displayName": "Label Font Size", + "description": "Set the font size of the labels. Default: 4\n", + "paramType": "NUMBER", + "paramGroup": "Gene Name Label", + "paramValues": null, + "defaultValue": 4, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "label_font_type", + "displayName": "Label Font Type", + "description": "Set the font type of the labels. Default: 1\n", + "paramType": "NUMBER", + "paramGroup": "Gene Name Label", + "paramValues": null, + "defaultValue": 1, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "displace_feature_labels", + "displayName": "Displace Feature Labels", + "description": "Set to TRUE to displace gene labels. Default: FALSE. Set TRUE if you want to displace\nthe feature (gene) label for a specific set of features. Make sure to use custom x- and y- limits and give\nsufficient space for displacement; otherwise other labels than the desired ones will appear displaced.\n", + "paramType": "BOOLEAN", + "paramGroup": "Gene Name Label", + "paramValues": null, + "defaultValue": false, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "custom_gene_list_special_label_displacement", + "displayName": "Gene List Special Label Displacement", + "description": "Provide a list of features (comma separated) for which you want\nspecial displacement of the feature label.\n", + "paramType": "STRING", + "paramGroup": "Gene Name Label", + "paramValues": null, + "defaultValue": "", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "special_label_displacement_x_axis", + "displayName": "Special Label Displacement (X-Axis)", + "description": "Displacement of the feature label on the x-axis. Default: 2\n", + "paramType": "NUMBER", + "paramGroup": "Gene Name Label", + "paramValues": null, + "defaultValue": 2, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "special_label_displacement_y_axis", + "displayName": "Special Label Displacement (Y-Axis)", + "description": "Displacement of the feature label on the y-axis. Default: 2\n", + "paramType": "NUMBER", + "paramGroup": "Gene Name Label", + "paramValues": null, + "defaultValue": 2, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "color_of_signif_threshold_line", + "displayName": "Color of P-Value Threshold Line", + "description": "Color of the significance threshold line. Default: \"blue\"\n", + "paramType": "SELECT", + "paramGroup": "Plot", + "paramValues": [ + "white", + "aliceblue", + "antiquewhite", + "antiquewhite1", + "antiquewhite2", + "antiquewhite3", + "antiquewhite4", + "aquamarine", + "aquamarine1", + "aquamarine2", + "aquamarine3", + "aquamarine4", + "azure", + "azure1", + "azure2", + "azure3", + "azure4", + "beige", + "bisque", + "bisque1", + "bisque2", + "bisque3", + "bisque4", + "black", + "blanchedalmond", + "blue", + "blue1", + "blue2", + "blue3", + "blue4", + "blueviolet", + "brown", + "brown1", + "brown2", + "brown3", + "brown4", + "burlywood", + "burlywood1", + "burlywood2", + "burlywood3", + "burlywood4", + "cadetblue", + "cadetblue1", + "cadetblue2", + "cadetblue3", + "cadetblue4", + "chartreuse", + "chartreuse1", + "chartreuse2", + "chartreuse3", + "chartreuse4", + "chocolate", + "chocolate1", + "chocolate2", + "chocolate3", + "chocolate4", + "coral", + "coral1", + "coral2", + "coral3", + "coral4", + "cornflowerblue", + "cornsilk", + "cornsilk1", + "cornsilk2", + "cornsilk3", + "cornsilk4", + "cyan", + "cyan1", + "cyan2", + "cyan3", + "cyan4", + "darkblue", + "darkcyan", + "darkgoldenrod", + "darkgoldenrod1", + "darkgoldenrod2", + "darkgoldenrod3", + "darkgoldenrod4", + "darkgray", + "darkgreen", + "darkgrey", + "darkkhaki", + "darkmagenta", + "darkolivegreen", + "darkolivegreen1", + "darkolivegreen2", + "darkolivegreen3", + "darkolivegreen4", + "darkorange", + "darkorange1", + "darkorange2", + "darkorange3", + "darkorange4", + "darkorchid", + "darkorchid1", + "darkorchid2", + "darkorchid3", + "darkorchid4", + "darkred", + "darksalmon", + "darkseagreen", + "darkseagreen1", + "darkseagreen2", + "darkseagreen3", + "darkseagreen4", + "darkslateblue", + "darkslategray", + "darkslategray1", + "darkslategray2", + "darkslategray3", + "darkslategray4", + "darkslategrey", + "darkturquoise", + "darkviolet", + "deeppink", + "deeppink1", + "deeppink2", + "deeppink3", + "deeppink4", + "deepskyblue", + "deepskyblue1", + "deepskyblue2", + "deepskyblue3", + "deepskyblue4", + "dimgray", + "dimgrey", + "dodgerblue", + "dodgerblue1", + "dodgerblue2", + "dodgerblue3", + "dodgerblue4", + "firebrick", + "firebrick1", + "firebrick2", + "firebrick3", + "firebrick4", + "floralwhite", + "forestgreen", + "gainsboro", + "ghostwhite", + "gold", + "gold1", + "gold2", + "gold3", + "gold4", + "goldenrod", + "goldenrod1", + "goldenrod2", + "goldenrod3", + "goldenrod4", + "gray", + "gray0", + "gray1", + "gray2", + "gray3", + "gray4", + "gray5", + "gray6", + "gray7", + "gray8", + "gray9", + "gray10", + "gray11", + "gray12", + "gray13", + "gray14", + "gray15", + "gray16", + "gray17", + "gray18", + "gray19", + "gray20", + "gray21", + "gray22", + "gray23", + "gray24", + "gray25", + "gray26", + "gray27", + "gray28", + "gray29", + "gray30", + "gray31", + "gray32", + "gray33", + "gray34", + "gray35", + "gray36", + "gray37", + "gray38", + "gray39", + "gray40", + "gray41", + "gray42", + "gray43", + "gray44", + "gray45", + "gray46", + "gray47", + "gray48", + "gray49", + "gray50", + "gray51", + "gray52", + "gray53", + "gray54", + "gray55", + "gray56", + "gray57", + "gray58", + "gray59", + "gray60", + "gray61", + "gray62", + "gray63", + "gray64", + "gray65", + "gray66", + "gray67", + "gray68", + "gray69", + "gray70", + "gray71", + "gray72", + "gray73", + "gray74", + "gray75", + "gray76", + "gray77", + "gray78", + "gray79", + "gray80", + "gray81", + "gray82", + "gray83", + "gray84", + "gray85", + "gray86", + "gray87", + "gray88", + "gray89", + "gray90", + "gray91", + "gray92", + "gray93", + "gray94", + "gray95", + "gray96", + "gray97", + "gray98", + "gray99", + "gray100", + "green", + "green1", + "green2", + "green3", + "green4", + "greenyellow", + "grey", + "grey0", + "grey1", + "grey2", + "grey3", + "grey4", + "grey5", + "grey6", + "grey7", + "grey8", + "grey9", + "grey10", + "grey11", + "grey12", + "grey13", + "grey14", + "grey15", + "grey16", + "grey17", + "grey18", + "grey19", + "grey20", + "grey21", + "grey22", + "grey23", + "grey24", + "grey25", + "grey26", + "grey27", + "grey28", + "grey29", + "grey30", + "grey31", + "grey32", + "grey33", + "grey34", + "grey35", + "grey36", + "grey37", + "grey38", + "grey39", + "grey40", + "grey41", + "grey42", + "grey43", + "grey44", + "grey45", + "grey46", + "grey47", + "grey48", + "grey49", + "grey50", + "grey51", + "grey52", + "grey53", + "grey54", + "grey55", + "grey56", + "grey57", + "grey58", + "grey59", + "grey60", + "grey61", + "grey62", + "grey63", + "grey64", + "grey65", + "grey66", + "grey67", + "grey68", + "grey69", + "grey70", + "grey71", + "grey72", + "grey73", + "grey74", + "grey75", + "grey76", + "grey77", + "grey78", + "grey79", + "grey80", + "grey81", + "grey82", + "grey83", + "grey84", + "grey85", + "grey86", + "grey87", + "grey88", + "grey89", + "grey90", + "grey91", + "grey92", + "grey93", + "grey94", + "grey95", + "grey96", + "grey97", + "grey98", + "grey99", + "grey100", + "honeydew", + "honeydew1", + "honeydew2", + "honeydew3", + "honeydew4", + "hotpink", + "hotpink1", + "hotpink2", + "hotpink3", + "hotpink4", + "indianred", + "indianred1", + "indianred2", + "indianred3", + "indianred4", + "ivory", + "ivory1", + "ivory2", + "ivory3", + "ivory4", + "khaki", + "khaki1", + "khaki2", + "khaki3", + "khaki4", + "lavender", + "lavenderblush", + "lavenderblush1", + "lavenderblush2", + "lavenderblush3", + "lavenderblush4", + "lawngreen", + "lemonchiffon", + "lemonchiffon1", + "lemonchiffon2", + "lemonchiffon3", + "lemonchiffon4", + "lightblue", + "lightblue1", + "lightblue2", + "lightblue3", + "lightblue4", + "lightcoral", + "lightcyan", + "lightcyan1", + "lightcyan2", + "lightcyan3", + "lightcyan4", + "lightgoldenrod", + "lightgoldenrod1", + "lightgoldenrod2", + "lightgoldenrod3", + "lightgoldenrod4", + "lightgoldenrodyellow", + "lightgray", + "lightgreen", + "lightgrey", + "lightpink", + "lightpink1", + "lightpink2", + "lightpink3", + "lightpink4", + "lightsalmon", + "lightsalmon1", + "lightsalmon2", + "lightsalmon3", + "lightsalmon4", + "lightseagreen", + "lightskyblue", + "lightskyblue1", + "lightskyblue2", + "lightskyblue3", + "lightskyblue4", + "lightslateblue", + "lightslategray", + "lightslategrey", + "lightsteelblue", + "lightsteelblue1", + "lightsteelblue2", + "lightsteelblue3", + "lightsteelblue4", + "lightyellow", + "lightyellow1", + "lightyellow2", + "lightyellow3", + "lightyellow4", + "limegreen", + "linen", + "magenta", + "magenta1", + "magenta2", + "magenta3", + "magenta4", + "maroon", + "maroon1", + "maroon2", + "maroon3", + "maroon4", + "mediumaquamarine", + "mediumblue", + "mediumorchid", + "mediumorchid1", + "mediumorchid2", + "mediumorchid3", + "mediumorchid4", + "mediumpurple", + "mediumpurple1", + "mediumpurple2", + "mediumpurple3", + "mediumpurple4", + "mediumseagreen", + "mediumslateblue", + "mediumspringgreen", + "mediumturquoise", + "mediumvioletred", + "midnightblue", + "mintcream", + "mistyrose", + "mistyrose1", + "mistyrose2", + "mistyrose3", + "mistyrose4", + "moccasin", + "navajowhite", + "navajowhite1", + "navajowhite2", + "navajowhite3", + "navajowhite4", + "navy", + "navyblue", + "oldlace", + "olivedrab", + "olivedrab1", + "olivedrab2", + "olivedrab3", + "olivedrab4", + "orange", + "orange1", + "orange2", + "orange3", + "orange4", + "orangered", + "orangered1", + "orangered2", + "orangered3", + "orangered4", + "orchid", + "orchid1", + "orchid2", + "orchid3", + "orchid4", + "palegoldenrod", + "palegreen", + "palegreen1", + "palegreen2", + "palegreen3", + "palegreen4", + "paleturquoise", + "paleturquoise1", + "paleturquoise2", + "paleturquoise3", + "paleturquoise4", + "palevioletred", + "palevioletred1", + "palevioletred2", + "palevioletred3", + "palevioletred4", + "papayawhip", + "peachpuff", + "peachpuff1", + "peachpuff2", + "peachpuff3", + "peachpuff4", + "peru", + "pink", + "pink1", + "pink2", + "pink3", + "pink4", + "plum", + "plum1", + "plum2", + "plum3", + "plum4", + "powderblue", + "purple", + "purple1", + "purple2", + "purple3", + "purple4", + "red", + "red1", + "red2", + "red3", + "red4", + "rosybrown", + "rosybrown1", + "rosybrown2", + "rosybrown3", + "rosybrown4", + "royalblue", + "royalblue1", + "royalblue2", + "royalblue3", + "royalblue4", + "saddlebrown", + "salmon", + "salmon1", + "salmon2", + "salmon3", + "salmon4", + "sandybrown", + "seagreen", + "seagreen1", + "seagreen2", + "seagreen3", + "seagreen4", + "seashell", + "seashell1", + "seashell2", + "seashell3", + "seashell4", + "sienna", + "sienna1", + "sienna2", + "sienna3", + "sienna4", + "skyblue", + "skyblue1", + "skyblue2", + "skyblue3", + "skyblue4", + "slateblue", + "slateblue1", + "slateblue2", + "slateblue3", + "slateblue4", + "slategray", + "slategray1", + "slategray2", + "slategray3", + "slategray4", + "slategrey", + "snow", + "snow1", + "snow2", + "snow3", + "snow4", + "springgreen", + "springgreen1", + "springgreen2", + "springgreen3", + "springgreen4", + "steelblue", + "steelblue1", + "steelblue2", + "steelblue3", + "steelblue4", + "tan", + "tan1", + "tan2", + "tan3", + "tan4", + "thistle", + "thistle1", + "thistle2", + "thistle3", + "thistle4", + "tomato", + "tomato1", + "tomato2", + "tomato3", + "tomato4", + "turquoise", + "turquoise1", + "turquoise2", + "turquoise3", + "turquoise4", + "violet", + "violetred", + "violetred1", + "violetred2", + "violetred3", + "violetred4", + "wheat", + "wheat1", + "wheat2", + "wheat3", + "wheat4", + "whitesmoke", + "yellow", + "yellow1", + "yellow2", + "yellow3", + "yellow4", + "yellowgreen" + ], + "defaultValue": "blue", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "color_of_non_significant_features", + "displayName": "Color of Non-Significant Features", + "description": "Color of the non-significant features. Default: \"black\"\n", + "paramType": "SELECT", + "paramGroup": "Plot", + "paramValues": [ + "white", + "aliceblue", + "antiquewhite", + "antiquewhite1", + "antiquewhite2", + "antiquewhite3", + "antiquewhite4", + "aquamarine", + "aquamarine1", + "aquamarine2", + "aquamarine3", + "aquamarine4", + "azure", + "azure1", + "azure2", + "azure3", + "azure4", + "beige", + "bisque", + "bisque1", + "bisque2", + "bisque3", + "bisque4", + "black", + "blanchedalmond", + "blue", + "blue1", + "blue2", + "blue3", + "blue4", + "blueviolet", + "brown", + "brown1", + "brown2", + "brown3", + "brown4", + "burlywood", + "burlywood1", + "burlywood2", + "burlywood3", + "burlywood4", + "cadetblue", + "cadetblue1", + "cadetblue2", + "cadetblue3", + "cadetblue4", + "chartreuse", + "chartreuse1", + "chartreuse2", + "chartreuse3", + "chartreuse4", + "chocolate", + "chocolate1", + "chocolate2", + "chocolate3", + "chocolate4", + "coral", + "coral1", + "coral2", + "coral3", + "coral4", + "cornflowerblue", + "cornsilk", + "cornsilk1", + "cornsilk2", + "cornsilk3", + "cornsilk4", + "cyan", + "cyan1", + "cyan2", + "cyan3", + "cyan4", + "darkblue", + "darkcyan", + "darkgoldenrod", + "darkgoldenrod1", + "darkgoldenrod2", + "darkgoldenrod3", + "darkgoldenrod4", + "darkgray", + "darkgreen", + "darkgrey", + "darkkhaki", + "darkmagenta", + "darkolivegreen", + "darkolivegreen1", + "darkolivegreen2", + "darkolivegreen3", + "darkolivegreen4", + "darkorange", + "darkorange1", + "darkorange2", + "darkorange3", + "darkorange4", + "darkorchid", + "darkorchid1", + "darkorchid2", + "darkorchid3", + "darkorchid4", + "darkred", + "darksalmon", + "darkseagreen", + "darkseagreen1", + "darkseagreen2", + "darkseagreen3", + "darkseagreen4", + "darkslateblue", + "darkslategray", + "darkslategray1", + "darkslategray2", + "darkslategray3", + "darkslategray4", + "darkslategrey", + "darkturquoise", + "darkviolet", + "deeppink", + "deeppink1", + "deeppink2", + "deeppink3", + "deeppink4", + "deepskyblue", + "deepskyblue1", + "deepskyblue2", + "deepskyblue3", + "deepskyblue4", + "dimgray", + "dimgrey", + "dodgerblue", + "dodgerblue1", + "dodgerblue2", + "dodgerblue3", + "dodgerblue4", + "firebrick", + "firebrick1", + "firebrick2", + "firebrick3", + "firebrick4", + "floralwhite", + "forestgreen", + "gainsboro", + "ghostwhite", + "gold", + "gold1", + "gold2", + "gold3", + "gold4", + "goldenrod", + "goldenrod1", + "goldenrod2", + "goldenrod3", + "goldenrod4", + "gray", + "gray0", + "gray1", + "gray2", + "gray3", + "gray4", + "gray5", + "gray6", + "gray7", + "gray8", + "gray9", + "gray10", + "gray11", + "gray12", + "gray13", + "gray14", + "gray15", + "gray16", + "gray17", + "gray18", + "gray19", + "gray20", + "gray21", + "gray22", + "gray23", + "gray24", + "gray25", + "gray26", + "gray27", + "gray28", + "gray29", + "gray30", + "gray31", + "gray32", + "gray33", + "gray34", + "gray35", + "gray36", + "gray37", + "gray38", + "gray39", + "gray40", + "gray41", + "gray42", + "gray43", + "gray44", + "gray45", + "gray46", + "gray47", + "gray48", + "gray49", + "gray50", + "gray51", + "gray52", + "gray53", + "gray54", + "gray55", + "gray56", + "gray57", + "gray58", + "gray59", + "gray60", + "gray61", + "gray62", + "gray63", + "gray64", + "gray65", + "gray66", + "gray67", + "gray68", + "gray69", + "gray70", + "gray71", + "gray72", + "gray73", + "gray74", + "gray75", + "gray76", + "gray77", + "gray78", + "gray79", + "gray80", + "gray81", + "gray82", + "gray83", + "gray84", + "gray85", + "gray86", + "gray87", + "gray88", + "gray89", + "gray90", + "gray91", + "gray92", + "gray93", + "gray94", + "gray95", + "gray96", + "gray97", + "gray98", + "gray99", + "gray100", + "green", + "green1", + "green2", + "green3", + "green4", + "greenyellow", + "grey", + "grey0", + "grey1", + "grey2", + "grey3", + "grey4", + "grey5", + "grey6", + "grey7", + "grey8", + "grey9", + "grey10", + "grey11", + "grey12", + "grey13", + "grey14", + "grey15", + "grey16", + "grey17", + "grey18", + "grey19", + "grey20", + "grey21", + "grey22", + "grey23", + "grey24", + "grey25", + "grey26", + "grey27", + "grey28", + "grey29", + "grey30", + "grey31", + "grey32", + "grey33", + "grey34", + "grey35", + "grey36", + "grey37", + "grey38", + "grey39", + "grey40", + "grey41", + "grey42", + "grey43", + "grey44", + "grey45", + "grey46", + "grey47", + "grey48", + "grey49", + "grey50", + "grey51", + "grey52", + "grey53", + "grey54", + "grey55", + "grey56", + "grey57", + "grey58", + "grey59", + "grey60", + "grey61", + "grey62", + "grey63", + "grey64", + "grey65", + "grey66", + "grey67", + "grey68", + "grey69", + "grey70", + "grey71", + "grey72", + "grey73", + "grey74", + "grey75", + "grey76", + "grey77", + "grey78", + "grey79", + "grey80", + "grey81", + "grey82", + "grey83", + "grey84", + "grey85", + "grey86", + "grey87", + "grey88", + "grey89", + "grey90", + "grey91", + "grey92", + "grey93", + "grey94", + "grey95", + "grey96", + "grey97", + "grey98", + "grey99", + "grey100", + "honeydew", + "honeydew1", + "honeydew2", + "honeydew3", + "honeydew4", + "hotpink", + "hotpink1", + "hotpink2", + "hotpink3", + "hotpink4", + "indianred", + "indianred1", + "indianred2", + "indianred3", + "indianred4", + "ivory", + "ivory1", + "ivory2", + "ivory3", + "ivory4", + "khaki", + "khaki1", + "khaki2", + "khaki3", + "khaki4", + "lavender", + "lavenderblush", + "lavenderblush1", + "lavenderblush2", + "lavenderblush3", + "lavenderblush4", + "lawngreen", + "lemonchiffon", + "lemonchiffon1", + "lemonchiffon2", + "lemonchiffon3", + "lemonchiffon4", + "lightblue", + "lightblue1", + "lightblue2", + "lightblue3", + "lightblue4", + "lightcoral", + "lightcyan", + "lightcyan1", + "lightcyan2", + "lightcyan3", + "lightcyan4", + "lightgoldenrod", + "lightgoldenrod1", + "lightgoldenrod2", + "lightgoldenrod3", + "lightgoldenrod4", + "lightgoldenrodyellow", + "lightgray", + "lightgreen", + "lightgrey", + "lightpink", + "lightpink1", + "lightpink2", + "lightpink3", + "lightpink4", + "lightsalmon", + "lightsalmon1", + "lightsalmon2", + "lightsalmon3", + "lightsalmon4", + "lightseagreen", + "lightskyblue", + "lightskyblue1", + "lightskyblue2", + "lightskyblue3", + "lightskyblue4", + "lightslateblue", + "lightslategray", + "lightslategrey", + "lightsteelblue", + "lightsteelblue1", + "lightsteelblue2", + "lightsteelblue3", + "lightsteelblue4", + "lightyellow", + "lightyellow1", + "lightyellow2", + "lightyellow3", + "lightyellow4", + "limegreen", + "linen", + "magenta", + "magenta1", + "magenta2", + "magenta3", + "magenta4", + "maroon", + "maroon1", + "maroon2", + "maroon3", + "maroon4", + "mediumaquamarine", + "mediumblue", + "mediumorchid", + "mediumorchid1", + "mediumorchid2", + "mediumorchid3", + "mediumorchid4", + "mediumpurple", + "mediumpurple1", + "mediumpurple2", + "mediumpurple3", + "mediumpurple4", + "mediumseagreen", + "mediumslateblue", + "mediumspringgreen", + "mediumturquoise", + "mediumvioletred", + "midnightblue", + "mintcream", + "mistyrose", + "mistyrose1", + "mistyrose2", + "mistyrose3", + "mistyrose4", + "moccasin", + "navajowhite", + "navajowhite1", + "navajowhite2", + "navajowhite3", + "navajowhite4", + "navy", + "navyblue", + "oldlace", + "olivedrab", + "olivedrab1", + "olivedrab2", + "olivedrab3", + "olivedrab4", + "orange", + "orange1", + "orange2", + "orange3", + "orange4", + "orangered", + "orangered1", + "orangered2", + "orangered3", + "orangered4", + "orchid", + "orchid1", + "orchid2", + "orchid3", + "orchid4", + "palegoldenrod", + "palegreen", + "palegreen1", + "palegreen2", + "palegreen3", + "palegreen4", + "paleturquoise", + "paleturquoise1", + "paleturquoise2", + "paleturquoise3", + "paleturquoise4", + "palevioletred", + "palevioletred1", + "palevioletred2", + "palevioletred3", + "palevioletred4", + "papayawhip", + "peachpuff", + "peachpuff1", + "peachpuff2", + "peachpuff3", + "peachpuff4", + "peru", + "pink", + "pink1", + "pink2", + "pink3", + "pink4", + "plum", + "plum1", + "plum2", + "plum3", + "plum4", + "powderblue", + "purple", + "purple1", + "purple2", + "purple3", + "purple4", + "red", + "red1", + "red2", + "red3", + "red4", + "rosybrown", + "rosybrown1", + "rosybrown2", + "rosybrown3", + "rosybrown4", + "royalblue", + "royalblue1", + "royalblue2", + "royalblue3", + "royalblue4", + "saddlebrown", + "salmon", + "salmon1", + "salmon2", + "salmon3", + "salmon4", + "sandybrown", + "seagreen", + "seagreen1", + "seagreen2", + "seagreen3", + "seagreen4", + "seashell", + "seashell1", + "seashell2", + "seashell3", + "seashell4", + "sienna", + "sienna1", + "sienna2", + "sienna3", + "sienna4", + "skyblue", + "skyblue1", + "skyblue2", + "skyblue3", + "skyblue4", + "slateblue", + "slateblue1", + "slateblue2", + "slateblue3", + "slateblue4", + "slategray", + "slategray1", + "slategray2", + "slategray3", + "slategray4", + "slategrey", + "snow", + "snow1", + "snow2", + "snow3", + "snow4", + "springgreen", + "springgreen1", + "springgreen2", + "springgreen3", + "springgreen4", + "steelblue", + "steelblue1", + "steelblue2", + "steelblue3", + "steelblue4", + "tan", + "tan1", + "tan2", + "tan3", + "tan4", + "thistle", + "thistle1", + "thistle2", + "thistle3", + "thistle4", + "tomato", + "tomato1", + "tomato2", + "tomato3", + "tomato4", + "turquoise", + "turquoise1", + "turquoise2", + "turquoise3", + "turquoise4", + "violet", + "violetred", + "violetred1", + "violetred2", + "violetred3", + "violetred4", + "wheat", + "wheat1", + "wheat2", + "wheat3", + "wheat4", + "whitesmoke", + "yellow", + "yellow1", + "yellow2", + "yellow3", + "yellow4", + "yellowgreen" + ], + "defaultValue": "black", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "color_of_logfold_change_threshold_line", + "displayName": "Color of Log Fold Change Threshold Line", + "description": "Color of the log fold change threshold line. Default: \"red\"\n", + "paramType": "SELECT", + "paramGroup": "Plot", + "paramValues": [ + "white", + "aliceblue", + "antiquewhite", + "antiquewhite1", + "antiquewhite2", + "antiquewhite3", + "antiquewhite4", + "aquamarine", + "aquamarine1", + "aquamarine2", + "aquamarine3", + "aquamarine4", + "azure", + "azure1", + "azure2", + "azure3", + "azure4", + "beige", + "bisque", + "bisque1", + "bisque2", + "bisque3", + "bisque4", + "black", + "blanchedalmond", + "blue", + "blue1", + "blue2", + "blue3", + "blue4", + "blueviolet", + "brown", + "brown1", + "brown2", + "brown3", + "brown4", + "burlywood", + "burlywood1", + "burlywood2", + "burlywood3", + "burlywood4", + "cadetblue", + "cadetblue1", + "cadetblue2", + "cadetblue3", + "cadetblue4", + "chartreuse", + "chartreuse1", + "chartreuse2", + "chartreuse3", + "chartreuse4", + "chocolate", + "chocolate1", + "chocolate2", + "chocolate3", + "chocolate4", + "coral", + "coral1", + "coral2", + "coral3", + "coral4", + "cornflowerblue", + "cornsilk", + "cornsilk1", + "cornsilk2", + "cornsilk3", + "cornsilk4", + "cyan", + "cyan1", + "cyan2", + "cyan3", + "cyan4", + "darkblue", + "darkcyan", + "darkgoldenrod", + "darkgoldenrod1", + "darkgoldenrod2", + "darkgoldenrod3", + "darkgoldenrod4", + "darkgray", + "darkgreen", + "darkgrey", + "darkkhaki", + "darkmagenta", + "darkolivegreen", + "darkolivegreen1", + "darkolivegreen2", + "darkolivegreen3", + "darkolivegreen4", + "darkorange", + "darkorange1", + "darkorange2", + "darkorange3", + "darkorange4", + "darkorchid", + "darkorchid1", + "darkorchid2", + "darkorchid3", + "darkorchid4", + "darkred", + "darksalmon", + "darkseagreen", + "darkseagreen1", + "darkseagreen2", + "darkseagreen3", + "darkseagreen4", + "darkslateblue", + "darkslategray", + "darkslategray1", + "darkslategray2", + "darkslategray3", + "darkslategray4", + "darkslategrey", + "darkturquoise", + "darkviolet", + "deeppink", + "deeppink1", + "deeppink2", + "deeppink3", + "deeppink4", + "deepskyblue", + "deepskyblue1", + "deepskyblue2", + "deepskyblue3", + "deepskyblue4", + "dimgray", + "dimgrey", + "dodgerblue", + "dodgerblue1", + "dodgerblue2", + "dodgerblue3", + "dodgerblue4", + "firebrick", + "firebrick1", + "firebrick2", + "firebrick3", + "firebrick4", + "floralwhite", + "forestgreen", + "gainsboro", + "ghostwhite", + "gold", + "gold1", + "gold2", + "gold3", + "gold4", + "goldenrod", + "goldenrod1", + "goldenrod2", + "goldenrod3", + "goldenrod4", + "gray", + "gray0", + "gray1", + "gray2", + "gray3", + "gray4", + "gray5", + "gray6", + "gray7", + "gray8", + "gray9", + "gray10", + "gray11", + "gray12", + "gray13", + "gray14", + "gray15", + "gray16", + "gray17", + "gray18", + "gray19", + "gray20", + "gray21", + "gray22", + "gray23", + "gray24", + "gray25", + "gray26", + "gray27", + "gray28", + "gray29", + "gray30", + "gray31", + "gray32", + "gray33", + "gray34", + "gray35", + "gray36", + "gray37", + "gray38", + "gray39", + "gray40", + "gray41", + "gray42", + "gray43", + "gray44", + "gray45", + "gray46", + "gray47", + "gray48", + "gray49", + "gray50", + "gray51", + "gray52", + "gray53", + "gray54", + "gray55", + "gray56", + "gray57", + "gray58", + "gray59", + "gray60", + "gray61", + "gray62", + "gray63", + "gray64", + "gray65", + "gray66", + "gray67", + "gray68", + "gray69", + "gray70", + "gray71", + "gray72", + "gray73", + "gray74", + "gray75", + "gray76", + "gray77", + "gray78", + "gray79", + "gray80", + "gray81", + "gray82", + "gray83", + "gray84", + "gray85", + "gray86", + "gray87", + "gray88", + "gray89", + "gray90", + "gray91", + "gray92", + "gray93", + "gray94", + "gray95", + "gray96", + "gray97", + "gray98", + "gray99", + "gray100", + "green", + "green1", + "green2", + "green3", + "green4", + "greenyellow", + "grey", + "grey0", + "grey1", + "grey2", + "grey3", + "grey4", + "grey5", + "grey6", + "grey7", + "grey8", + "grey9", + "grey10", + "grey11", + "grey12", + "grey13", + "grey14", + "grey15", + "grey16", + "grey17", + "grey18", + "grey19", + "grey20", + "grey21", + "grey22", + "grey23", + "grey24", + "grey25", + "grey26", + "grey27", + "grey28", + "grey29", + "grey30", + "grey31", + "grey32", + "grey33", + "grey34", + "grey35", + "grey36", + "grey37", + "grey38", + "grey39", + "grey40", + "grey41", + "grey42", + "grey43", + "grey44", + "grey45", + "grey46", + "grey47", + "grey48", + "grey49", + "grey50", + "grey51", + "grey52", + "grey53", + "grey54", + "grey55", + "grey56", + "grey57", + "grey58", + "grey59", + "grey60", + "grey61", + "grey62", + "grey63", + "grey64", + "grey65", + "grey66", + "grey67", + "grey68", + "grey69", + "grey70", + "grey71", + "grey72", + "grey73", + "grey74", + "grey75", + "grey76", + "grey77", + "grey78", + "grey79", + "grey80", + "grey81", + "grey82", + "grey83", + "grey84", + "grey85", + "grey86", + "grey87", + "grey88", + "grey89", + "grey90", + "grey91", + "grey92", + "grey93", + "grey94", + "grey95", + "grey96", + "grey97", + "grey98", + "grey99", + "grey100", + "honeydew", + "honeydew1", + "honeydew2", + "honeydew3", + "honeydew4", + "hotpink", + "hotpink1", + "hotpink2", + "hotpink3", + "hotpink4", + "indianred", + "indianred1", + "indianred2", + "indianred3", + "indianred4", + "ivory", + "ivory1", + "ivory2", + "ivory3", + "ivory4", + "khaki", + "khaki1", + "khaki2", + "khaki3", + "khaki4", + "lavender", + "lavenderblush", + "lavenderblush1", + "lavenderblush2", + "lavenderblush3", + "lavenderblush4", + "lawngreen", + "lemonchiffon", + "lemonchiffon1", + "lemonchiffon2", + "lemonchiffon3", + "lemonchiffon4", + "lightblue", + "lightblue1", + "lightblue2", + "lightblue3", + "lightblue4", + "lightcoral", + "lightcyan", + "lightcyan1", + "lightcyan2", + "lightcyan3", + "lightcyan4", + "lightgoldenrod", + "lightgoldenrod1", + "lightgoldenrod2", + "lightgoldenrod3", + "lightgoldenrod4", + "lightgoldenrodyellow", + "lightgray", + "lightgreen", + "lightgrey", + "lightpink", + "lightpink1", + "lightpink2", + "lightpink3", + "lightpink4", + "lightsalmon", + "lightsalmon1", + "lightsalmon2", + "lightsalmon3", + "lightsalmon4", + "lightseagreen", + "lightskyblue", + "lightskyblue1", + "lightskyblue2", + "lightskyblue3", + "lightskyblue4", + "lightslateblue", + "lightslategray", + "lightslategrey", + "lightsteelblue", + "lightsteelblue1", + "lightsteelblue2", + "lightsteelblue3", + "lightsteelblue4", + "lightyellow", + "lightyellow1", + "lightyellow2", + "lightyellow3", + "lightyellow4", + "limegreen", + "linen", + "magenta", + "magenta1", + "magenta2", + "magenta3", + "magenta4", + "maroon", + "maroon1", + "maroon2", + "maroon3", + "maroon4", + "mediumaquamarine", + "mediumblue", + "mediumorchid", + "mediumorchid1", + "mediumorchid2", + "mediumorchid3", + "mediumorchid4", + "mediumpurple", + "mediumpurple1", + "mediumpurple2", + "mediumpurple3", + "mediumpurple4", + "mediumseagreen", + "mediumslateblue", + "mediumspringgreen", + "mediumturquoise", + "mediumvioletred", + "midnightblue", + "mintcream", + "mistyrose", + "mistyrose1", + "mistyrose2", + "mistyrose3", + "mistyrose4", + "moccasin", + "navajowhite", + "navajowhite1", + "navajowhite2", + "navajowhite3", + "navajowhite4", + "navy", + "navyblue", + "oldlace", + "olivedrab", + "olivedrab1", + "olivedrab2", + "olivedrab3", + "olivedrab4", + "orange", + "orange1", + "orange2", + "orange3", + "orange4", + "orangered", + "orangered1", + "orangered2", + "orangered3", + "orangered4", + "orchid", + "orchid1", + "orchid2", + "orchid3", + "orchid4", + "palegoldenrod", + "palegreen", + "palegreen1", + "palegreen2", + "palegreen3", + "palegreen4", + "paleturquoise", + "paleturquoise1", + "paleturquoise2", + "paleturquoise3", + "paleturquoise4", + "palevioletred", + "palevioletred1", + "palevioletred2", + "palevioletred3", + "palevioletred4", + "papayawhip", + "peachpuff", + "peachpuff1", + "peachpuff2", + "peachpuff3", + "peachpuff4", + "peru", + "pink", + "pink1", + "pink2", + "pink3", + "pink4", + "plum", + "plum1", + "plum2", + "plum3", + "plum4", + "powderblue", + "purple", + "purple1", + "purple2", + "purple3", + "purple4", + "red", + "red1", + "red2", + "red3", + "red4", + "rosybrown", + "rosybrown1", + "rosybrown2", + "rosybrown3", + "rosybrown4", + "royalblue", + "royalblue1", + "royalblue2", + "royalblue3", + "royalblue4", + "saddlebrown", + "salmon", + "salmon1", + "salmon2", + "salmon3", + "salmon4", + "sandybrown", + "seagreen", + "seagreen1", + "seagreen2", + "seagreen3", + "seagreen4", + "seashell", + "seashell1", + "seashell2", + "seashell3", + "seashell4", + "sienna", + "sienna1", + "sienna2", + "sienna3", + "sienna4", + "skyblue", + "skyblue1", + "skyblue2", + "skyblue3", + "skyblue4", + "slateblue", + "slateblue1", + "slateblue2", + "slateblue3", + "slateblue4", + "slategray", + "slategray1", + "slategray2", + "slategray3", + "slategray4", + "slategrey", + "snow", + "snow1", + "snow2", + "snow3", + "snow4", + "springgreen", + "springgreen1", + "springgreen2", + "springgreen3", + "springgreen4", + "steelblue", + "steelblue1", + "steelblue2", + "steelblue3", + "steelblue4", + "tan", + "tan1", + "tan2", + "tan3", + "tan4", + "thistle", + "thistle1", + "thistle2", + "thistle3", + "thistle4", + "tomato", + "tomato1", + "tomato2", + "tomato3", + "tomato4", + "turquoise", + "turquoise1", + "turquoise2", + "turquoise3", + "turquoise4", + "violet", + "violetred", + "violetred1", + "violetred2", + "violetred3", + "violetred4", + "wheat", + "wheat1", + "wheat2", + "wheat3", + "wheat4", + "whitesmoke", + "yellow", + "yellow1", + "yellow2", + "yellow3", + "yellow4", + "yellowgreen" + ], + "defaultValue": "red", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "color_of_features_meeting_only_signif_threshold", + "displayName": "Color of Features Meeting Only P-Value Threshold", + "description": "Color of the features that meet only the significance\nthreshold. Default: \"lightgoldenrod2\"\n", + "paramType": "SELECT", + "paramGroup": "Plot", + "paramValues": [ + "white", + "aliceblue", + "antiquewhite", + "antiquewhite1", + "antiquewhite2", + "antiquewhite3", + "antiquewhite4", + "aquamarine", + "aquamarine1", + "aquamarine2", + "aquamarine3", + "aquamarine4", + "azure", + "azure1", + "azure2", + "azure3", + "azure4", + "beige", + "bisque", + "bisque1", + "bisque2", + "bisque3", + "bisque4", + "black", + "blanchedalmond", + "blue", + "blue1", + "blue2", + "blue3", + "blue4", + "blueviolet", + "brown", + "brown1", + "brown2", + "brown3", + "brown4", + "burlywood", + "burlywood1", + "burlywood2", + "burlywood3", + "burlywood4", + "cadetblue", + "cadetblue1", + "cadetblue2", + "cadetblue3", + "cadetblue4", + "chartreuse", + "chartreuse1", + "chartreuse2", + "chartreuse3", + "chartreuse4", + "chocolate", + "chocolate1", + "chocolate2", + "chocolate3", + "chocolate4", + "coral", + "coral1", + "coral2", + "coral3", + "coral4", + "cornflowerblue", + "cornsilk", + "cornsilk1", + "cornsilk2", + "cornsilk3", + "cornsilk4", + "cyan", + "cyan1", + "cyan2", + "cyan3", + "cyan4", + "darkblue", + "darkcyan", + "darkgoldenrod", + "darkgoldenrod1", + "darkgoldenrod2", + "darkgoldenrod3", + "darkgoldenrod4", + "darkgray", + "darkgreen", + "darkgrey", + "darkkhaki", + "darkmagenta", + "darkolivegreen", + "darkolivegreen1", + "darkolivegreen2", + "darkolivegreen3", + "darkolivegreen4", + "darkorange", + "darkorange1", + "darkorange2", + "darkorange3", + "darkorange4", + "darkorchid", + "darkorchid1", + "darkorchid2", + "darkorchid3", + "darkorchid4", + "darkred", + "darksalmon", + "darkseagreen", + "darkseagreen1", + "darkseagreen2", + "darkseagreen3", + "darkseagreen4", + "darkslateblue", + "darkslategray", + "darkslategray1", + "darkslategray2", + "darkslategray3", + "darkslategray4", + "darkslategrey", + "darkturquoise", + "darkviolet", + "deeppink", + "deeppink1", + "deeppink2", + "deeppink3", + "deeppink4", + "deepskyblue", + "deepskyblue1", + "deepskyblue2", + "deepskyblue3", + "deepskyblue4", + "dimgray", + "dimgrey", + "dodgerblue", + "dodgerblue1", + "dodgerblue2", + "dodgerblue3", + "dodgerblue4", + "firebrick", + "firebrick1", + "firebrick2", + "firebrick3", + "firebrick4", + "floralwhite", + "forestgreen", + "gainsboro", + "ghostwhite", + "gold", + "gold1", + "gold2", + "gold3", + "gold4", + "goldenrod", + "goldenrod1", + "goldenrod2", + "goldenrod3", + "goldenrod4", + "gray", + "gray0", + "gray1", + "gray2", + "gray3", + "gray4", + "gray5", + "gray6", + "gray7", + "gray8", + "gray9", + "gray10", + "gray11", + "gray12", + "gray13", + "gray14", + "gray15", + "gray16", + "gray17", + "gray18", + "gray19", + "gray20", + "gray21", + "gray22", + "gray23", + "gray24", + "gray25", + "gray26", + "gray27", + "gray28", + "gray29", + "gray30", + "gray31", + "gray32", + "gray33", + "gray34", + "gray35", + "gray36", + "gray37", + "gray38", + "gray39", + "gray40", + "gray41", + "gray42", + "gray43", + "gray44", + "gray45", + "gray46", + "gray47", + "gray48", + "gray49", + "gray50", + "gray51", + "gray52", + "gray53", + "gray54", + "gray55", + "gray56", + "gray57", + "gray58", + "gray59", + "gray60", + "gray61", + "gray62", + "gray63", + "gray64", + "gray65", + "gray66", + "gray67", + "gray68", + "gray69", + "gray70", + "gray71", + "gray72", + "gray73", + "gray74", + "gray75", + "gray76", + "gray77", + "gray78", + "gray79", + "gray80", + "gray81", + "gray82", + "gray83", + "gray84", + "gray85", + "gray86", + "gray87", + "gray88", + "gray89", + "gray90", + "gray91", + "gray92", + "gray93", + "gray94", + "gray95", + "gray96", + "gray97", + "gray98", + "gray99", + "gray100", + "green", + "green1", + "green2", + "green3", + "green4", + "greenyellow", + "grey", + "grey0", + "grey1", + "grey2", + "grey3", + "grey4", + "grey5", + "grey6", + "grey7", + "grey8", + "grey9", + "grey10", + "grey11", + "grey12", + "grey13", + "grey14", + "grey15", + "grey16", + "grey17", + "grey18", + "grey19", + "grey20", + "grey21", + "grey22", + "grey23", + "grey24", + "grey25", + "grey26", + "grey27", + "grey28", + "grey29", + "grey30", + "grey31", + "grey32", + "grey33", + "grey34", + "grey35", + "grey36", + "grey37", + "grey38", + "grey39", + "grey40", + "grey41", + "grey42", + "grey43", + "grey44", + "grey45", + "grey46", + "grey47", + "grey48", + "grey49", + "grey50", + "grey51", + "grey52", + "grey53", + "grey54", + "grey55", + "grey56", + "grey57", + "grey58", + "grey59", + "grey60", + "grey61", + "grey62", + "grey63", + "grey64", + "grey65", + "grey66", + "grey67", + "grey68", + "grey69", + "grey70", + "grey71", + "grey72", + "grey73", + "grey74", + "grey75", + "grey76", + "grey77", + "grey78", + "grey79", + "grey80", + "grey81", + "grey82", + "grey83", + "grey84", + "grey85", + "grey86", + "grey87", + "grey88", + "grey89", + "grey90", + "grey91", + "grey92", + "grey93", + "grey94", + "grey95", + "grey96", + "grey97", + "grey98", + "grey99", + "grey100", + "honeydew", + "honeydew1", + "honeydew2", + "honeydew3", + "honeydew4", + "hotpink", + "hotpink1", + "hotpink2", + "hotpink3", + "hotpink4", + "indianred", + "indianred1", + "indianred2", + "indianred3", + "indianred4", + "ivory", + "ivory1", + "ivory2", + "ivory3", + "ivory4", + "khaki", + "khaki1", + "khaki2", + "khaki3", + "khaki4", + "lavender", + "lavenderblush", + "lavenderblush1", + "lavenderblush2", + "lavenderblush3", + "lavenderblush4", + "lawngreen", + "lemonchiffon", + "lemonchiffon1", + "lemonchiffon2", + "lemonchiffon3", + "lemonchiffon4", + "lightblue", + "lightblue1", + "lightblue2", + "lightblue3", + "lightblue4", + "lightcoral", + "lightcyan", + "lightcyan1", + "lightcyan2", + "lightcyan3", + "lightcyan4", + "lightgoldenrod", + "lightgoldenrod1", + "lightgoldenrod2", + "lightgoldenrod3", + "lightgoldenrod4", + "lightgoldenrodyellow", + "lightgray", + "lightgreen", + "lightgrey", + "lightpink", + "lightpink1", + "lightpink2", + "lightpink3", + "lightpink4", + "lightsalmon", + "lightsalmon1", + "lightsalmon2", + "lightsalmon3", + "lightsalmon4", + "lightseagreen", + "lightskyblue", + "lightskyblue1", + "lightskyblue2", + "lightskyblue3", + "lightskyblue4", + "lightslateblue", + "lightslategray", + "lightslategrey", + "lightsteelblue", + "lightsteelblue1", + "lightsteelblue2", + "lightsteelblue3", + "lightsteelblue4", + "lightyellow", + "lightyellow1", + "lightyellow2", + "lightyellow3", + "lightyellow4", + "limegreen", + "linen", + "magenta", + "magenta1", + "magenta2", + "magenta3", + "magenta4", + "maroon", + "maroon1", + "maroon2", + "maroon3", + "maroon4", + "mediumaquamarine", + "mediumblue", + "mediumorchid", + "mediumorchid1", + "mediumorchid2", + "mediumorchid3", + "mediumorchid4", + "mediumpurple", + "mediumpurple1", + "mediumpurple2", + "mediumpurple3", + "mediumpurple4", + "mediumseagreen", + "mediumslateblue", + "mediumspringgreen", + "mediumturquoise", + "mediumvioletred", + "midnightblue", + "mintcream", + "mistyrose", + "mistyrose1", + "mistyrose2", + "mistyrose3", + "mistyrose4", + "moccasin", + "navajowhite", + "navajowhite1", + "navajowhite2", + "navajowhite3", + "navajowhite4", + "navy", + "navyblue", + "oldlace", + "olivedrab", + "olivedrab1", + "olivedrab2", + "olivedrab3", + "olivedrab4", + "orange", + "orange1", + "orange2", + "orange3", + "orange4", + "orangered", + "orangered1", + "orangered2", + "orangered3", + "orangered4", + "orchid", + "orchid1", + "orchid2", + "orchid3", + "orchid4", + "palegoldenrod", + "palegreen", + "palegreen1", + "palegreen2", + "palegreen3", + "palegreen4", + "paleturquoise", + "paleturquoise1", + "paleturquoise2", + "paleturquoise3", + "paleturquoise4", + "palevioletred", + "palevioletred1", + "palevioletred2", + "palevioletred3", + "palevioletred4", + "papayawhip", + "peachpuff", + "peachpuff1", + "peachpuff2", + "peachpuff3", + "peachpuff4", + "peru", + "pink", + "pink1", + "pink2", + "pink3", + "pink4", + "plum", + "plum1", + "plum2", + "plum3", + "plum4", + "powderblue", + "purple", + "purple1", + "purple2", + "purple3", + "purple4", + "red", + "red1", + "red2", + "red3", + "red4", + "rosybrown", + "rosybrown1", + "rosybrown2", + "rosybrown3", + "rosybrown4", + "royalblue", + "royalblue1", + "royalblue2", + "royalblue3", + "royalblue4", + "saddlebrown", + "salmon", + "salmon1", + "salmon2", + "salmon3", + "salmon4", + "sandybrown", + "seagreen", + "seagreen1", + "seagreen2", + "seagreen3", + "seagreen4", + "seashell", + "seashell1", + "seashell2", + "seashell3", + "seashell4", + "sienna", + "sienna1", + "sienna2", + "sienna3", + "sienna4", + "skyblue", + "skyblue1", + "skyblue2", + "skyblue3", + "skyblue4", + "slateblue", + "slateblue1", + "slateblue2", + "slateblue3", + "slateblue4", + "slategray", + "slategray1", + "slategray2", + "slategray3", + "slategray4", + "slategrey", + "snow", + "snow1", + "snow2", + "snow3", + "snow4", + "springgreen", + "springgreen1", + "springgreen2", + "springgreen3", + "springgreen4", + "steelblue", + "steelblue1", + "steelblue2", + "steelblue3", + "steelblue4", + "tan", + "tan1", + "tan2", + "tan3", + "tan4", + "thistle", + "thistle1", + "thistle2", + "thistle3", + "thistle4", + "tomato", + "tomato1", + "tomato2", + "tomato3", + "tomato4", + "turquoise", + "turquoise1", + "turquoise2", + "turquoise3", + "turquoise4", + "violet", + "violetred", + "violetred1", + "violetred2", + "violetred3", + "violetred4", + "wheat", + "wheat1", + "wheat2", + "wheat3", + "wheat4", + "whitesmoke", + "yellow", + "yellow1", + "yellow2", + "yellow3", + "yellow4", + "yellowgreen" + ], + "defaultValue": "lightgoldenrod2", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "color_for_features_meeting_pvalue_and_foldchange_thresholds", + "displayName": "Color for features meeting p-value and fold-change thresholds", + "description": "Color of the features that meet both the p-value\nand fold change thresholds. Default: \"red\"\n", + "paramType": "SELECT", + "paramGroup": "Plot", + "paramValues": [ + "white", + "aliceblue", + "antiquewhite", + "antiquewhite1", + "antiquewhite2", + "antiquewhite3", + "antiquewhite4", + "aquamarine", + "aquamarine1", + "aquamarine2", + "aquamarine3", + "aquamarine4", + "azure", + "azure1", + "azure2", + "azure3", + "azure4", + "beige", + "bisque", + "bisque1", + "bisque2", + "bisque3", + "bisque4", + "black", + "blanchedalmond", + "blue", + "blue1", + "blue2", + "blue3", + "blue4", + "blueviolet", + "brown", + "brown1", + "brown2", + "brown3", + "brown4", + "burlywood", + "burlywood1", + "burlywood2", + "burlywood3", + "burlywood4", + "cadetblue", + "cadetblue1", + "cadetblue2", + "cadetblue3", + "cadetblue4", + "chartreuse", + "chartreuse1", + "chartreuse2", + "chartreuse3", + "chartreuse4", + "chocolate", + "chocolate1", + "chocolate2", + "chocolate3", + "chocolate4", + "coral", + "coral1", + "coral2", + "coral3", + "coral4", + "cornflowerblue", + "cornsilk", + "cornsilk1", + "cornsilk2", + "cornsilk3", + "cornsilk4", + "cyan", + "cyan1", + "cyan2", + "cyan3", + "cyan4", + "darkblue", + "darkcyan", + "darkgoldenrod", + "darkgoldenrod1", + "darkgoldenrod2", + "darkgoldenrod3", + "darkgoldenrod4", + "darkgray", + "darkgreen", + "darkgrey", + "darkkhaki", + "darkmagenta", + "darkolivegreen", + "darkolivegreen1", + "darkolivegreen2", + "darkolivegreen3", + "darkolivegreen4", + "darkorange", + "darkorange1", + "darkorange2", + "darkorange3", + "darkorange4", + "darkorchid", + "darkorchid1", + "darkorchid2", + "darkorchid3", + "darkorchid4", + "darkred", + "darksalmon", + "darkseagreen", + "darkseagreen1", + "darkseagreen2", + "darkseagreen3", + "darkseagreen4", + "darkslateblue", + "darkslategray", + "darkslategray1", + "darkslategray2", + "darkslategray3", + "darkslategray4", + "darkslategrey", + "darkturquoise", + "darkviolet", + "deeppink", + "deeppink1", + "deeppink2", + "deeppink3", + "deeppink4", + "deepskyblue", + "deepskyblue1", + "deepskyblue2", + "deepskyblue3", + "deepskyblue4", + "dimgray", + "dimgrey", + "dodgerblue", + "dodgerblue1", + "dodgerblue2", + "dodgerblue3", + "dodgerblue4", + "firebrick", + "firebrick1", + "firebrick2", + "firebrick3", + "firebrick4", + "floralwhite", + "forestgreen", + "gainsboro", + "ghostwhite", + "gold", + "gold1", + "gold2", + "gold3", + "gold4", + "goldenrod", + "goldenrod1", + "goldenrod2", + "goldenrod3", + "goldenrod4", + "gray", + "gray0", + "gray1", + "gray2", + "gray3", + "gray4", + "gray5", + "gray6", + "gray7", + "gray8", + "gray9", + "gray10", + "gray11", + "gray12", + "gray13", + "gray14", + "gray15", + "gray16", + "gray17", + "gray18", + "gray19", + "gray20", + "gray21", + "gray22", + "gray23", + "gray24", + "gray25", + "gray26", + "gray27", + "gray28", + "gray29", + "gray30", + "gray31", + "gray32", + "gray33", + "gray34", + "gray35", + "gray36", + "gray37", + "gray38", + "gray39", + "gray40", + "gray41", + "gray42", + "gray43", + "gray44", + "gray45", + "gray46", + "gray47", + "gray48", + "gray49", + "gray50", + "gray51", + "gray52", + "gray53", + "gray54", + "gray55", + "gray56", + "gray57", + "gray58", + "gray59", + "gray60", + "gray61", + "gray62", + "gray63", + "gray64", + "gray65", + "gray66", + "gray67", + "gray68", + "gray69", + "gray70", + "gray71", + "gray72", + "gray73", + "gray74", + "gray75", + "gray76", + "gray77", + "gray78", + "gray79", + "gray80", + "gray81", + "gray82", + "gray83", + "gray84", + "gray85", + "gray86", + "gray87", + "gray88", + "gray89", + "gray90", + "gray91", + "gray92", + "gray93", + "gray94", + "gray95", + "gray96", + "gray97", + "gray98", + "gray99", + "gray100", + "green", + "green1", + "green2", + "green3", + "green4", + "greenyellow", + "grey", + "grey0", + "grey1", + "grey2", + "grey3", + "grey4", + "grey5", + "grey6", + "grey7", + "grey8", + "grey9", + "grey10", + "grey11", + "grey12", + "grey13", + "grey14", + "grey15", + "grey16", + "grey17", + "grey18", + "grey19", + "grey20", + "grey21", + "grey22", + "grey23", + "grey24", + "grey25", + "grey26", + "grey27", + "grey28", + "grey29", + "grey30", + "grey31", + "grey32", + "grey33", + "grey34", + "grey35", + "grey36", + "grey37", + "grey38", + "grey39", + "grey40", + "grey41", + "grey42", + "grey43", + "grey44", + "grey45", + "grey46", + "grey47", + "grey48", + "grey49", + "grey50", + "grey51", + "grey52", + "grey53", + "grey54", + "grey55", + "grey56", + "grey57", + "grey58", + "grey59", + "grey60", + "grey61", + "grey62", + "grey63", + "grey64", + "grey65", + "grey66", + "grey67", + "grey68", + "grey69", + "grey70", + "grey71", + "grey72", + "grey73", + "grey74", + "grey75", + "grey76", + "grey77", + "grey78", + "grey79", + "grey80", + "grey81", + "grey82", + "grey83", + "grey84", + "grey85", + "grey86", + "grey87", + "grey88", + "grey89", + "grey90", + "grey91", + "grey92", + "grey93", + "grey94", + "grey95", + "grey96", + "grey97", + "grey98", + "grey99", + "grey100", + "honeydew", + "honeydew1", + "honeydew2", + "honeydew3", + "honeydew4", + "hotpink", + "hotpink1", + "hotpink2", + "hotpink3", + "hotpink4", + "indianred", + "indianred1", + "indianred2", + "indianred3", + "indianred4", + "ivory", + "ivory1", + "ivory2", + "ivory3", + "ivory4", + "khaki", + "khaki1", + "khaki2", + "khaki3", + "khaki4", + "lavender", + "lavenderblush", + "lavenderblush1", + "lavenderblush2", + "lavenderblush3", + "lavenderblush4", + "lawngreen", + "lemonchiffon", + "lemonchiffon1", + "lemonchiffon2", + "lemonchiffon3", + "lemonchiffon4", + "lightblue", + "lightblue1", + "lightblue2", + "lightblue3", + "lightblue4", + "lightcoral", + "lightcyan", + "lightcyan1", + "lightcyan2", + "lightcyan3", + "lightcyan4", + "lightgoldenrod", + "lightgoldenrod1", + "lightgoldenrod2", + "lightgoldenrod3", + "lightgoldenrod4", + "lightgoldenrodyellow", + "lightgray", + "lightgreen", + "lightgrey", + "lightpink", + "lightpink1", + "lightpink2", + "lightpink3", + "lightpink4", + "lightsalmon", + "lightsalmon1", + "lightsalmon2", + "lightsalmon3", + "lightsalmon4", + "lightseagreen", + "lightskyblue", + "lightskyblue1", + "lightskyblue2", + "lightskyblue3", + "lightskyblue4", + "lightslateblue", + "lightslategray", + "lightslategrey", + "lightsteelblue", + "lightsteelblue1", + "lightsteelblue2", + "lightsteelblue3", + "lightsteelblue4", + "lightyellow", + "lightyellow1", + "lightyellow2", + "lightyellow3", + "lightyellow4", + "limegreen", + "linen", + "magenta", + "magenta1", + "magenta2", + "magenta3", + "magenta4", + "maroon", + "maroon1", + "maroon2", + "maroon3", + "maroon4", + "mediumaquamarine", + "mediumblue", + "mediumorchid", + "mediumorchid1", + "mediumorchid2", + "mediumorchid3", + "mediumorchid4", + "mediumpurple", + "mediumpurple1", + "mediumpurple2", + "mediumpurple3", + "mediumpurple4", + "mediumseagreen", + "mediumslateblue", + "mediumspringgreen", + "mediumturquoise", + "mediumvioletred", + "midnightblue", + "mintcream", + "mistyrose", + "mistyrose1", + "mistyrose2", + "mistyrose3", + "mistyrose4", + "moccasin", + "navajowhite", + "navajowhite1", + "navajowhite2", + "navajowhite3", + "navajowhite4", + "navy", + "navyblue", + "oldlace", + "olivedrab", + "olivedrab1", + "olivedrab2", + "olivedrab3", + "olivedrab4", + "orange", + "orange1", + "orange2", + "orange3", + "orange4", + "orangered", + "orangered1", + "orangered2", + "orangered3", + "orangered4", + "orchid", + "orchid1", + "orchid2", + "orchid3", + "orchid4", + "palegoldenrod", + "palegreen", + "palegreen1", + "palegreen2", + "palegreen3", + "palegreen4", + "paleturquoise", + "paleturquoise1", + "paleturquoise2", + "paleturquoise3", + "paleturquoise4", + "palevioletred", + "palevioletred1", + "palevioletred2", + "palevioletred3", + "palevioletred4", + "papayawhip", + "peachpuff", + "peachpuff1", + "peachpuff2", + "peachpuff3", + "peachpuff4", + "peru", + "pink", + "pink1", + "pink2", + "pink3", + "pink4", + "plum", + "plum1", + "plum2", + "plum3", + "plum4", + "powderblue", + "purple", + "purple1", + "purple2", + "purple3", + "purple4", + "red", + "red1", + "red2", + "red3", + "red4", + "rosybrown", + "rosybrown1", + "rosybrown2", + "rosybrown3", + "rosybrown4", + "royalblue", + "royalblue1", + "royalblue2", + "royalblue3", + "royalblue4", + "saddlebrown", + "salmon", + "salmon1", + "salmon2", + "salmon3", + "salmon4", + "sandybrown", + "seagreen", + "seagreen1", + "seagreen2", + "seagreen3", + "seagreen4", + "seashell", + "seashell1", + "seashell2", + "seashell3", + "seashell4", + "sienna", + "sienna1", + "sienna2", + "sienna3", + "sienna4", + "skyblue", + "skyblue1", + "skyblue2", + "skyblue3", + "skyblue4", + "slateblue", + "slateblue1", + "slateblue2", + "slateblue3", + "slateblue4", + "slategray", + "slategray1", + "slategray2", + "slategray3", + "slategray4", + "slategrey", + "snow", + "snow1", + "snow2", + "snow3", + "snow4", + "springgreen", + "springgreen1", + "springgreen2", + "springgreen3", + "springgreen4", + "steelblue", + "steelblue1", + "steelblue2", + "steelblue3", + "steelblue4", + "tan", + "tan1", + "tan2", + "tan3", + "tan4", + "thistle", + "thistle1", + "thistle2", + "thistle3", + "thistle4", + "tomato", + "tomato1", + "tomato2", + "tomato3", + "tomato4", + "turquoise", + "turquoise1", + "turquoise2", + "turquoise3", + "turquoise4", + "violet", + "violetred", + "violetred1", + "violetred2", + "violetred3", + "violetred4", + "wheat", + "wheat1", + "wheat2", + "wheat3", + "wheat4", + "whitesmoke", + "yellow", + "yellow1", + "yellow2", + "yellow3", + "yellow4", + "yellowgreen" + ], + "defaultValue": "red", + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "flip_vplot", + "displayName": "Flip Contrast", + "description": "Set to TRUE to flip the fold change values so that the volcano plot looks like a comparison was\nB-A. Default: FALSE\n", + "paramType": "BOOLEAN", + "paramGroup": "Plot", + "paramValues": null, + "defaultValue": false, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "use_default_x_axis_limit", + "displayName": "Use Default X-Axis Limit", + "description": "Set to TRUE to use the default x-axis limit. Default: TRUE\n", + "paramType": "BOOLEAN", + "paramGroup": "Plot", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "x_axis_limit", + "displayName": "X-Axis Limit", + "description": "Custom x-axis limit. Default: c(-5, 5)\n", + "paramType": "NUMBER", + "paramGroup": "Plot", + "paramValues": null, + "defaultValue": 5, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "use_default_y_axis_limit", + "displayName": "Use Default Y-Axis Limit", + "description": "Set to TRUE to use the default y-axis limit. Default: TRUE\n", + "paramType": "BOOLEAN", + "paramGroup": "Plot", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "y_axis_limit", + "displayName": "Y-Axis Limit", + "description": "Custom y-axis limit. Default: c(0, 10)\n", + "paramType": "NUMBER", + "paramGroup": "Plot", + "paramValues": null, + "defaultValue": 10, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "point_size", + "displayName": "Point Size", + "description": "Size of the points in the plot. Default: 1\n", + "paramType": "NUMBER", + "paramGroup": "Plot", + "paramValues": null, + "defaultValue": 2, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "add_deg_columns", + "displayName": "Add DEG Columns to Output Table", + "description": "Add additional columns from the DEG analysis to the\noutput dataset. Default: `\"FC\", \"logFC\", \"tstat\", \"pval\", \"adjpval\"`", + "paramType": "MULTISELECT", + "paramGroup": "Table", + "paramValues": [ + "FC", + "logFC", + "tstat", + "pval", + "adjpval" + ], + "defaultValue": ["FC", "logFC", "tstat", "pval", "adjpval"], + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "image_width", + "displayName": "Image Width", + "description": "output image width in pixels - only used if save_plots is TRUE\n", + "paramType": "NUMBER", + "paramGroup": "Image", + "paramValues": null, + "defaultValue": 15, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "image_height", + "displayName": "Image Height", + "description": "output image height in pixels - only used if save_plots is TRUE\n", + "paramType": "NUMBER", + "paramGroup": "Image", + "paramValues": null, + "defaultValue": 15, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "dpi", + "displayName": "Image Resolution", + "description": "dots-per-inch of the output image (see `ggsave()`) - only used if save_plots is TRUE\n", + "paramType": "NUMBER", + "paramGroup": "Image", + "paramValues": null, + "defaultValue": 300, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "use_default_grid_layout", + "displayName": "Use Default Grid Layout", + "description": "Set to TRUE to use the default grid layout. Default: TRUE\n", + "paramType": "BOOLEAN", + "paramGroup": "Image", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "number_of_rows_in_grid_layout", + "displayName": "Number of Rows in Grid Layout", + "description": "Number of rows in the grid layout. Default: 1\n", + "paramType": "NUMBER", + "paramGroup": "Image", + "paramValues": null, + "defaultValue": 1, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "aspect_ratio", + "displayName": "Figure Aspect Ratio", + "description": "Aspect ratio of the output image. Default: 4/3\n", + "paramType": "NUMBER", + "paramGroup": "Image", + "paramValues": null, + "defaultValue": 0, + "condition": null, + "content": null, + "objectPropertyReference": null + }, + { + "key": "save_plots", + "displayName": "Save Plots", + "description": "Whether to save plots to files during analysis (Defaults to `TRUE`, overwritable using option 'moo_save_plots' or environment variable 'MOO_SAVE_PLOTS')\n", + "paramType": "BOOLEAN", + "paramGroup": "Visualization", + "paramValues": null, + "defaultValue": true, + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "outputs": { + "DataFrame": { + "type": "file", + "name": "summary_dataframe.rds" + }, + "figures": { + "type": "file", + "name": "figures/diff/volcano_summary.png" + } + } +} diff --git a/code/MOSuite/inst/extdata/galaxy/2_blueprints/write_multiOmicDataSet_properties.json b/code/MOSuite/inst/extdata/galaxy/2_blueprints/write_multiOmicDataSet_properties.json new file mode 100644 index 0000000..3dd9a5f --- /dev/null +++ b/code/MOSuite/inst/extdata/galaxy/2_blueprints/write_multiOmicDataSet_properties.json @@ -0,0 +1,52 @@ +{ + "r_function": "write_multiOmicDataSet_properties", + "title": "Write multiOmicDataSet Properties\n", + "description": "Writes the properties of a multiOmicDataSet object to disk as separate files in output_dir.\nProperties that are data frames are saved as CSV files, while all other objects are saved as RDS files.\n", + "columns": [], + "inputDatasets": [ + { + "key": "moo_input_rds", + "displayName": "MOO input Rds", + "description": "File path to the input multiOmicDataSet (MOO) RDS file.", + "paramType": "STRING", + "paramGroup": "basic", + "paramValues": null, + "defaultValue": "moo.rds", + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "parameters": [ + { + "key": "output_dir", + "displayName": "Output Directory", + "description": "Directory where the properties will be saved (default: \"moo\")\n", + "paramType": "STRING", + "paramGroup": "Basic", + "paramValues": null, + "defaultValue": "moo", + "condition": null, + "content": null, + "objectPropertyReference": null + } + ], + "outputs": { + "sample_metadata": { + "type": "file", + "name": "sample_metadata.csv" + }, + "feature_annotation": { + "type": "file", + "name": "feature_annotation.csv" + }, + "counts": { + "type": "directory", + "name": "counts/" + }, + "analyses": { + "type": "directory", + "name": "analyses/" + } + } +} diff --git a/code/MOSuite/inst/extdata/galaxy/galaxy.R b/code/MOSuite/inst/extdata/galaxy/galaxy.R new file mode 100644 index 0000000..3d92b9f --- /dev/null +++ b/code/MOSuite/inst/extdata/galaxy/galaxy.R @@ -0,0 +1,263 @@ +library(dplyr) + +#' @keywords internal +#' @examples +#' +#' get_function_meta("batch_correct_counts", tools::Rd_db("MOSuite")) +#' +get_function_meta <- function(func_name, rd_db) { + func_db <- rd_db[[paste0(func_name, ".Rd")]] + + title <- tools:::.Rd_get_metadata(func_db, "title") |> trimws() + desc <- paste( + tools:::.Rd_get_metadata(func_db, "description"), + tools:::.Rd_get_metadata(func_db, "details"), + sep = "\n\n" + ) |> + trimws() + arg_desc <- dplyr::as_tibble( + tools:::.Rd_get_argument_table(func_db), + .name_repair = "unique_quiet" + ) + colnames(arg_desc) <- c("arg", "desc") + arg_docs <- arg_desc |> + dplyr::pull("desc") |> + trimws() |> + as.list() + names(arg_docs) <- arg_desc |> dplyr::pull("arg") + options( + moo_print_plots = TRUE, + moo_save_plots = TRUE, + moo_plots_dir = "./figures", + print_plots = TRUE, # need if this function is defined outside the package's R source directory + save_plots = TRUE, + plots_dir = "./figures" + ) + arg_defaults <- lapply( + formals(func_name, envir = getNamespace("MOSuite")), + \(x) { + if (inherits(x, "name")) { + default <- NULL + } else if (inherits(x, "call")) { + default <- eval(x, envir = getNamespace("MOSuite")) + } else { + default <- x + } + return(default) + } + ) + if ("..." %in% names(arg_defaults)) { + arg_defaults <- arg_defaults |> + within(rm("...")) # remove `...` argument + } + args_meta <- names(arg_defaults) |> + lapply(\(arg) { + return(list( + defaultValue = arg_defaults[[arg]], + description = arg_docs[[arg]] + )) + }) + names(args_meta) <- names(arg_defaults) + + return(list( + r_function = func_name, + title = title, + description = desc, + args = args_meta + )) +} + +#' @keywords internal +get_function_args <- function(func_meta) { + func_names <- Filter( + \(x) !stringr::str_starts(x, "moo"), + names(func_meta$args) + ) + func_args <- lapply(func_names, \(x) func_meta$args[[x]][["defaultValue"]]) + + if (stringr::str_starts(names(func_meta$args)[1], "moo")) { + func_names <- c("moo_input_rds", "moo_output_rds", func_names) + func_args <- c("moo.rds", "moo.rds", func_args) + } + names(func_args) <- func_names + + return(func_args) +} + +#' @keywords internal +#' @examples +#' +#' update_function_template( +#' system.file("extdata", "galaxy", "template-templates", "create_multiOmicDataSet_from_files.json", +#' package = "MOSuite" +#' ), +#' tools::Rd_db("MOSuite") +#' ) +#' +update_function_template <- function( + template, + func_meta, + keep_deprecated_args = TRUE +) { + if (!rlang::is_installed("Rd2md")) { + stop("Required pacakge {Rd2md} is not installed") + } + + safe_rd_to_md <- function(x) { + if (is.null(x) || length(x) == 0) { + return("") + } + x_chr <- as.character(x) + if (length(x_chr) == 0 || all(is.na(x_chr))) { + return("") + } + return(tryCatch( + Rd2md::rd_str_to_md(x_chr), + error = function(e) { + paste(x_chr, collapse = "\n") + } + )) + } + + new_template <- list( + r_function = template$r_function, + title = safe_rd_to_md(template$title), + description = safe_rd_to_md(func_meta$description), + columns = list(), + inputDatasets = list(), + parameters = list(), + outputs = template$outputs + ) + args_in_template <- c() + template_args_missing <- c() + for (arg_type in c("columns", "inputDatasets", "parameters")) { + for (i in seq_along(template[[arg_type]])) { + arg_name <- template[[arg_type]][[i]]$key + if (arg_name %in% names(func_meta$args)) { + arg_meta <- template[[arg_type]][[i]] + arg_meta$description <- safe_rd_to_md( + func_meta$args[[arg_name]]$description + ) + arg_meta$defaultValue <- func_meta$args[[arg_name]]$defaultValue + args_in_template <- c(args_in_template, arg_name) + new_template[[arg_type]][[ + length(new_template[[arg_type]]) + 1 + ]] <- arg_meta + } else { + template_args_missing <- c(template_args_missing, arg_name) + if (isTRUE(keep_deprecated_args)) { + arg_meta <- template[[arg_type]][[i]] + new_template[[arg_type]][[ + length(new_template[[arg_type]]) + 1 + ]] <- arg_meta + } + } + } + } + if (length(template_args_missing) > 0) { + message(glue::glue( + "{template$r_function}: ", + "Argument(s) from template not found in R function doc: ", + "{paste(template_args_missing, collapse = ', ')}" + )) + } + + func_args_missing <- setdiff(names(func_meta$args), args_in_template) + if (length(func_args_missing) > 0) { + message( + glue::glue( + "{template$r_function}: ", + "Argument(s) from R function doc not found in template: ", + "{paste(func_args_missing, collapse = ', ')}" + ) + ) + } + return(new_template) +} + +#' @keywords internal +check_classes <- function(updated_template) { + for (p in updated_template$parameters) { + for (el in p) { + message(paste(p["key"], class(el))) + } + } + return() +} + +#' `jsonlite::write_json()` with preferred defaults +#' +#' @keywords internal +write_json <- function( + x, + filepath, + auto_unbox = TRUE, + pretty = TRUE, + null = "null", + na = "null", + ... +) { + return(invisible(jsonlite::write_json( + x, + filepath, + auto_unbox = auto_unbox, + pretty = pretty, + null = null, + na = na, + ... + ))) +} + +#' @keywords internal +write_package_json_blueprints <- + function( + input_dir = file.path("inst", "extdata", "galaxy", "1_mosuite-templates"), + blueprints_output_dir = file.path( + "inst", + "extdata", + "galaxy", + "2_blueprints" + ), + defaults_output_dir = file.path("inst", "extdata", "json_args", "defaults") + ) { + options( + moo_print_plots = TRUE, + moo_save_plots = TRUE, + moo_plots_dir = "./figures", + print_plots = TRUE, # need if this function is defined outside the package's R source directory + save_plots = TRUE, + plots_dir = "./figures" + ) + templates <- list.files( + input_dir, + pattern = ".*\\.json$", + full.names = TRUE + ) + rd_db <- tools::Rd_db("MOSuite") + for (f in templates) { + base_filename <- basename(f) + message(glue::glue("* Processing {base_filename}")) + + template <- jsonlite::read_json(f) + r_function <- template$r_function + func_meta <- get_function_meta(r_function, rd_db) + + # write default arguments + func_args <- get_function_args(func_meta) + write_json( + func_args, + file.path(defaults_output_dir, glue::glue("{r_function}.json")) + ) + + # write galaxy blueprint template + updated_template <- update_function_template( + template, + func_meta + ) + write_json( + updated_template, + file.path(blueprints_output_dir, glue::glue("{r_function}.json")) + ) + } + return(invisible()) + } diff --git a/code/MOSuite/inst/extdata/json_args/common/batch_correct_counts.json b/code/MOSuite/inst/extdata/json_args/common/batch_correct_counts.json new file mode 100644 index 0000000..c128597 --- /dev/null +++ b/code/MOSuite/inst/extdata/json_args/common/batch_correct_counts.json @@ -0,0 +1,16 @@ +{ + "moo_input_rds": "moo_norm.rds", + "moo_output_rds": "moo_batch.rds", + "count_type": "norm", + "sub_count_type": "voom", + "sample_id_colname": null, + "feature_id_colname": null, + "samples_to_include": null, + "covariates_colnames": "Group", + "batch_colname": "Batch", + "label_colname": "Label", + "colors_for_plots": null, + "print_plots": true, + "save_plots": true, + "plots_subdir": "batch" +} diff --git a/code/MOSuite/inst/extdata/json_args/common/clean_raw_counts.json b/code/MOSuite/inst/extdata/json_args/common/clean_raw_counts.json new file mode 100644 index 0000000..e11a4fb --- /dev/null +++ b/code/MOSuite/inst/extdata/json_args/common/clean_raw_counts.json @@ -0,0 +1,14 @@ +{ + "moo_input_rds": "moo_create.rds", + "moo_output_rds": "moo_clean.rds", + "count_type": "raw", + "sample_id_colname": null, + "feature_id_colname": null, + "samples_to_rename": "", + "cleanup_column_names": true, + "split_gene_name": true, + "aggregate_rows_with_duplicate_gene_names": true, + "gene_name_column_to_use_for_collapsing_duplicates": "", + "print_plots": true, + "save_plots": true +} diff --git a/code/MOSuite/inst/extdata/json_args/common/create_multiOmicDataSet_from_files.json b/code/MOSuite/inst/extdata/json_args/common/create_multiOmicDataSet_from_files.json new file mode 100644 index 0000000..7fc474a --- /dev/null +++ b/code/MOSuite/inst/extdata/json_args/common/create_multiOmicDataSet_from_files.json @@ -0,0 +1,5 @@ +{ + "feature_counts_filepath": "Raw_Counts.csv.gz", + "sample_meta_filepath": "Sample_Metadata_Bulk_RNA-seq_Training_Dataset_CCBR.csv.gz", + "moo_output_rds": "moo_create.rds" +} diff --git a/code/MOSuite/inst/extdata/json_args/common/diff_counts.json b/code/MOSuite/inst/extdata/json_args/common/diff_counts.json new file mode 100644 index 0000000..700bf35 --- /dev/null +++ b/code/MOSuite/inst/extdata/json_args/common/diff_counts.json @@ -0,0 +1,25 @@ +{ + "moo_input_rds": "moo_batch.rds", + "moo_output_rds": "moo_diff.rds", + "count_type": "filt", + "sub_count_type": null, + "sample_id_colname": null, + "feature_id_colname": null, + "samples_to_include": null, + "covariates_colnames": [ + "Group", + "Batch" + ], + "contrast_colname": "Group", + "contrasts": [ + "B-A", + "C-A", + "B-C" + ], + "input_in_log_counts": false, + "return_mean_and_sd": true, + "voom_normalization_method": "quantile", + "print_plots": true, + "save_plots": true, + "plots_subdir": "diff" +} diff --git a/code/MOSuite/inst/extdata/json_args/common/filter_counts.json b/code/MOSuite/inst/extdata/json_args/common/filter_counts.json new file mode 100644 index 0000000..0e71be4 --- /dev/null +++ b/code/MOSuite/inst/extdata/json_args/common/filter_counts.json @@ -0,0 +1,48 @@ +{ + "moo_input_rds": "moo_clean.rds", + "moo_output_rds": "moo_filter.rds", + "count_type": "clean", + "feature_id_colname": null, + "sample_id_colname": null, + "group_colname": "Group", + "label_colname": null, + "use_cpm_counts_to_filter": true, + "minimum_count_value_to_be_considered_nonzero": 8.0, + "minimum_number_of_samples_with_nonzero_counts_in_total": 7.0, + "use_group_based_filtering": false, + "minimum_number_of_samples_with_nonzero_counts_in_a_group": 3.0, + "principal_component_on_x_axis": 1.0, + "principal_component_on_y_axis": 2.0, + "legend_position_for_pca": "top", + "point_size_for_pca": 1.0, + "add_label_to_pca": true, + "label_font_size": 3.0, + "label_offset_x_": 2.0, + "label_offset_y_": 2.0, + "samples_to_rename": null, + "color_histogram_by_group": false, + "set_min_max_for_x_axis_for_histogram": false, + "minimum_for_x_axis_for_histogram": -1.0, + "maximum_for_x_axis_for_histogram": 1.0, + "legend_font_size_for_histogram": 10.0, + "legend_position_for_histogram": "top", + "number_of_histogram_legend_columns": 6.0, + "colors_for_plots": [ + "#5954d6", + "#e1562c", + "#b80058", + "#00c6f8", + "#d163e6", + "#00a76c", + "#ff9287", + "#008cf9", + "#006e00", + "#796880", + "#FFA500", + "#878500" + ], + "interactive_plots": false, + "save_plots": true, + "plot_corr_matrix_heatmap": true, + "samples_to_include": null +} diff --git a/code/MOSuite/inst/extdata/json_args/common/filter_diff.json b/code/MOSuite/inst/extdata/json_args/common/filter_diff.json new file mode 100644 index 0000000..bc41bd7 --- /dev/null +++ b/code/MOSuite/inst/extdata/json_args/common/filter_diff.json @@ -0,0 +1,38 @@ +{ + "moo_input_rds": "moo_diff.rds", + "moo_output_rds": "moo_diff_filter.rds", + "feature_id_colname": null, + "significance_column": "adjpval", + "significance_cutoff": 0.05, + "change_column": "logFC", + "change_cutoff": 1, + "filtering_mode": "any", + "include_estimates": [ + "FC", + "logFC", + "tstat", + "pval", + "adjpval" + ], + "round_estimates": true, + "rounding_decimal_for_percent_cells": 0, + "contrast_filter": "none", + "contrasts": null, + "groups": null, + "groups_filter": "none", + "label_font_size": 6, + "label_distance": 1, + "y_axis_expansion": 0.08, + "fill_colors": [ + "steelblue1", + "whitesmoke" + ], + "pie_chart_in_3d": true, + "bar_width": 0.4, + "draw_bar_border": true, + "plot_type": "bar", + "plot_titles_fontsize": 12, + "print_plots": true, + "save_plots": true, + "plots_subdir": "diff/filt" +} diff --git a/code/MOSuite/inst/extdata/json_args/common/normalize_counts.json b/code/MOSuite/inst/extdata/json_args/common/normalize_counts.json new file mode 100644 index 0000000..a5acdb5 --- /dev/null +++ b/code/MOSuite/inst/extdata/json_args/common/normalize_counts.json @@ -0,0 +1,33 @@ +{ + "moo_input_rds": "moo_filter.rds", + "moo_output_rds": "moo_norm.rds", + "count_type": "filt", + "norm_type": "voom", + "feature_id_colname": null, + "samples_to_include": null, + "sample_id_colname": null, + "group_colname": "Group", + "label_colname": null, + "input_in_log_counts": false, + "voom_normalization_method": "quantile", + "samples_to_rename": "", + "add_label_to_pca": true, + "principal_component_on_x_axis": 1, + "principal_component_on_y_axis": 2, + "legend_position_for_pca": "top", + "label_offset_x_": 2, + "label_offset_y_": 2, + "label_font_size": 3, + "point_size_for_pca": 8, + "color_histogram_by_group": true, + "set_min_max_for_x_axis_for_histogram": false, + "minimum_for_x_axis_for_histogram": -1, + "maximum_for_x_axis_for_histogram": 1, + "legend_font_size_for_histogram": 10, + "legend_position_for_histogram": "top", + "colors_for_plots": null, + "print_plots": true, + "save_plots": true, + "interactive_plots": false, + "plots_subdir": "norm" +} diff --git a/code/MOSuite/inst/extdata/json_args/common/plot_expr_heatmap.json b/code/MOSuite/inst/extdata/json_args/common/plot_expr_heatmap.json new file mode 100644 index 0000000..b1dc1f3 --- /dev/null +++ b/code/MOSuite/inst/extdata/json_args/common/plot_expr_heatmap.json @@ -0,0 +1,80 @@ +{ + "moo_input_rds": "moo_norm.rds", + "count_type": "norm", + "sub_count_type": "voom", + "sample_metadata": null, + "sample_id_colname": null, + "feature_id_colname": null, + "group_colname": "Group", + "label_colname": null, + "samples_to_include": null, + "color_values": [ + "#5954d6", + "#e1562c", + "#b80058", + "#00c6f8", + "#d163e6", + "#00a76c", + "#ff9287", + "#008cf9", + "#006e00", + "#796880", + "#FFA500", + "#878500" + ], + "include_all_genes": false, + "filter_top_genes_by_variance": true, + "top_genes_by_variance_to_include": 500, + "specific_genes_to_include_in_heatmap": "None", + "cluster_genes": true, + "gene_distance_metric": "correlation", + "gene_clustering_method": "average", + "display_gene_dendrograms": true, + "display_gene_names": false, + "center_and_rescale_expression": true, + "cluster_samples": false, + "arrange_sample_columns": true, + "order_by_gene_expression": false, + "gene_to_order_columns": " ", + "gene_expression_order": "low_to_high", + "smpl_distance_metric": "correlation", + "smpl_clustering_method": "average", + "display_smpl_dendrograms": true, + "reorder_dendrogram": false, + "reorder_dendrogram_order": null, + "display_sample_names": true, + "group_columns": [ + "Group", + "Replicate", + "Batch" + ], + "assign_group_colors": false, + "assign_color_to_sample_groups": null, + "group_colors": [ + "#5954d6", + "#e1562c", + "#b80058", + "#00c6f8", + "#d163e6", + "#00a76c", + "#ff9287", + "#008cf9", + "#006e00", + "#796880", + "#FFA500", + "#878500" + ], + "heatmap_color_scheme": "Default", + "autoscale_heatmap_color": true, + "set_min_heatmap_color": -2, + "set_max_heatmap_color": 2, + "aspect_ratio": "Auto", + "legend_font_size": 10, + "gene_name_font_size": 4, + "sample_name_font_size": 8, + "display_numbers": false, + "plot_filename": "expr_heatmap.png", + "print_plots": true, + "save_plots": true, + "plots_subdir": "heatmap" +} diff --git a/code/MOSuite/inst/extdata/json_args/common/plot_pca_2d.json b/code/MOSuite/inst/extdata/json_args/common/plot_pca_2d.json new file mode 100644 index 0000000..ab25827 --- /dev/null +++ b/code/MOSuite/inst/extdata/json_args/common/plot_pca_2d.json @@ -0,0 +1,36 @@ +{ + "moo_input_rds": "moo_norm.rds", + "sample_metadata": null, + "feature_id_colname": null, + "sample_id_colname": null, + "samples_to_rename": null, + "group_colname": "Group", + "label_colname": "Label", + "principal_components": [ + 1, + 2 + ], + "point_size": 1, + "add_label": true, + "label_font_size": 3, + "legend_position": "top", + "color_values": [ + "#5954d6", + "#e1562c", + "#b80058", + "#00c6f8", + "#d163e6", + "#00a76c", + "#ff9287", + "#008cf9", + "#006e00", + "#796880", + "#FFA500", + "#878500" + ], + "interactive_plots": false, + "plot_filename": "pca_2D.png", + "print_plots": true, + "save_plots": true, + "plots_subdir": "pca" +} \ No newline at end of file diff --git a/code/MOSuite/inst/extdata/json_args/common/plot_pca_3d.json b/code/MOSuite/inst/extdata/json_args/common/plot_pca_3d.json new file mode 100644 index 0000000..308d197 --- /dev/null +++ b/code/MOSuite/inst/extdata/json_args/common/plot_pca_3d.json @@ -0,0 +1,31 @@ +{ + "moo_input_rds": "moo_norm.rds", + "sample_metadata": null, + "feature_id_colname": null, + "sample_id_colname": null, + "samples_to_rename": null, + "group_colname": "Group", + "label_colname": "Label", + "principal_components": [1, 2, 3], + "point_size": 8, + "label_font_size": 24, + "color_values": [ + "#5954d6", + "#e1562c", + "#b80058", + "#00c6f8", + "#d163e6", + "#00a76c", + "#ff9287", + "#008cf9", + "#006e00", + "#796880", + "#FFA500", + "#878500" + ], + "plot_title": "PCA 3D", + "plot_filename": "pca_3D.html", + "print_plots": true, + "save_plots": true, + "plots_subdir": "pca" +} diff --git a/code/MOSuite/inst/extdata/json_args/common/plot_venn_diagram.json b/code/MOSuite/inst/extdata/json_args/common/plot_venn_diagram.json new file mode 100644 index 0000000..2c3b334 --- /dev/null +++ b/code/MOSuite/inst/extdata/json_args/common/plot_venn_diagram.json @@ -0,0 +1,40 @@ +{ + "moo_input_rds": "volcano_summary_dat.rds", + "moo_output_rds": "venn_diagram_dat.rds", + "feature_id_colname": null, + "contrasts_colname": "Contrast", + "select_contrasts": null, + "plot_type": "Venn diagram", + "intersection_ids": null, + "venn_force_unique": true, + "venn_numbers_format": "raw", + "venn_significant_digits": 2, + "venn_fill_colors": [ + "darkgoldenrod2", + "darkolivegreen2", + "mediumpurple3", + "darkorange2", + "lightgreen" + ], + "venn_fill_transparency": 0.2, + "venn_border_colors": "fill colors", + "venn_font_size_for_category_names": 3, + "venn_category_names_distance": null, + "venn_category_names_position": null, + "venn_font_size_for_counts": 6, + "venn_outer_margin": 0, + "intersections_order": "degree", + "display_empty_intersections": false, + "intersection_bar_color": "steelblue4", + "intersection_point_size": 2.2, + "intersection_line_width": 0.7, + "table_font_size": 0.7, + "table_content": "all intersections", + "dpi": 300, + "image_width": 4000, + "image_height": 3000, + "plot_filename": "venn_diagram.png", + "print_plots": true, + "save_plots": true, + "plots_subdir": "diff" +} diff --git a/code/MOSuite/inst/extdata/json_args/common/plot_volcano_enhanced.json b/code/MOSuite/inst/extdata/json_args/common/plot_volcano_enhanced.json new file mode 100644 index 0000000..960d6be --- /dev/null +++ b/code/MOSuite/inst/extdata/json_args/common/plot_volcano_enhanced.json @@ -0,0 +1,33 @@ +{ + "moo_input_rds": "moo_diff_filter.rds", + "moo_output_rds": "volcano_enhanced_dat.rds", + "feature_id_colname": null, + "signif_colname": ["B-A_adjpval", "B-C_adjpval"], + "signif_threshold": 0.05, + "change_colname": ["B-A_logFC", "B-C_logFC"], + "change_threshold": 1, + "value_to_sort_the_output_dataset": "p-value", + "num_features_to_label": 30, + "use_only_addition_labels": false, + "additional_labels": "", + "is_red": true, + "lab_size": 4, + "change_sig_name": "p-value", + "change_lfc_name": "log2FC", + "title": "Volcano Plots", + "use_custom_lab": false, + "ylim": 0, + "custom_xlim": "", + "xlim_additional": 0, + "ylim_additional": 0, + "axis_lab_size": 24, + "point_size": 2, + "image_width": 3000, + "image_height": 3000, + "dpi": 300, + "interactive_plots": false, + "print_plots": true, + "save_plots": true, + "plots_subdir": "diff", + "plot_filename": "volcano_enhanced.png" +} diff --git a/code/MOSuite/inst/extdata/json_args/common/plot_volcano_summary.json b/code/MOSuite/inst/extdata/json_args/common/plot_volcano_summary.json new file mode 100644 index 0000000..ee16ff7 --- /dev/null +++ b/code/MOSuite/inst/extdata/json_args/common/plot_volcano_summary.json @@ -0,0 +1,52 @@ +{ + "moo_input_rds": "moo_diff_filter.rds", + "moo_output_rds": "volcano_summary_dat.rds", + "feature_id_colname": null, + "signif_colname": "pval", + "signif_threshold": 0.05, + "change_threshold": 1, + "value_to_sort_the_output_dataset": "t-statistic", + "num_features_to_label": 30, + "add_features": false, + "label_features": false, + "custom_gene_list": "", + "default_label_color": "black", + "custom_label_color": "green3", + "label_x_adj": 0.2, + "label_y_adj": 0.2, + "line_thickness": 0.5, + "label_font_size": 4, + "label_font_type": 1, + "displace_feature_labels": false, + "custom_gene_list_special_label_displacement": "", + "special_label_displacement_x_axis": 2, + "special_label_displacement_y_axis": 2, + "color_of_signif_threshold_line": "blue", + "color_of_non_significant_features": "black", + "color_of_logfold_change_threshold_line": "red", + "color_of_features_meeting_only_signif_threshold": "lightgoldenrod2", + "color_for_features_meeting_pvalue_and_foldchange_thresholds": "red", + "flip_vplot": false, + "use_default_x_axis_limit": true, + "x_axis_limit": 5, + "use_default_y_axis_limit": true, + "y_axis_limit": 10, + "point_size": 2, + "add_deg_columns": [ + "FC", + "logFC", + "tstat", + "pval", + "adjpval" + ], + "image_width": 15, + "image_height": 15, + "dpi": 300, + "use_default_grid_layout": true, + "number_of_rows_in_grid_layout": 1, + "aspect_ratio": 0, + "plot_filename": "volcano_summary.png", + "print_plots": true, + "save_plots": true, + "plots_subdir": "diff" +} \ No newline at end of file diff --git a/code/MOSuite/inst/extdata/json_args/common/write_multiOmicDataSet_properties.json b/code/MOSuite/inst/extdata/json_args/common/write_multiOmicDataSet_properties.json new file mode 100644 index 0000000..61b1d34 --- /dev/null +++ b/code/MOSuite/inst/extdata/json_args/common/write_multiOmicDataSet_properties.json @@ -0,0 +1,6 @@ +{ + "moo_input_rds": "moo_diff_filter.rds", + "output_dir": { + "defaultValue": "moo" + } +} \ No newline at end of file diff --git a/code/MOSuite/inst/extdata/json_args/defaults/batch_correct_counts.json b/code/MOSuite/inst/extdata/json_args/defaults/batch_correct_counts.json new file mode 100644 index 0000000..fe8d42e --- /dev/null +++ b/code/MOSuite/inst/extdata/json_args/defaults/batch_correct_counts.json @@ -0,0 +1,16 @@ +{ + "moo_input_rds": "moo.rds", + "moo_output_rds": "moo.rds", + "count_type": "norm", + "sub_count_type": "voom", + "sample_id_colname": null, + "feature_id_colname": null, + "samples_to_include": null, + "covariates_colnames": "Group", + "batch_colname": "Batch", + "label_colname": null, + "colors_for_plots": null, + "print_plots": true, + "save_plots": true, + "plots_subdir": "batch" +} diff --git a/code/MOSuite/inst/extdata/json_args/defaults/clean_raw_counts.json b/code/MOSuite/inst/extdata/json_args/defaults/clean_raw_counts.json new file mode 100644 index 0000000..43c5568 --- /dev/null +++ b/code/MOSuite/inst/extdata/json_args/defaults/clean_raw_counts.json @@ -0,0 +1,15 @@ +{ + "moo_input_rds": "moo.rds", + "moo_output_rds": "moo.rds", + "count_type": "raw", + "sample_id_colname": null, + "feature_id_colname": null, + "samples_to_rename": "", + "cleanup_column_names": true, + "split_gene_name": true, + "aggregate_rows_with_duplicate_gene_names": true, + "gene_name_column_to_use_for_collapsing_duplicates": "", + "print_plots": true, + "save_plots": true, + "plots_subdir": "clean" +} diff --git a/code/MOSuite/inst/extdata/json_args/defaults/create_multiOmicDataSet_from_files.json b/code/MOSuite/inst/extdata/json_args/defaults/create_multiOmicDataSet_from_files.json new file mode 100644 index 0000000..02c0e00 --- /dev/null +++ b/code/MOSuite/inst/extdata/json_args/defaults/create_multiOmicDataSet_from_files.json @@ -0,0 +1,8 @@ +{ + "sample_meta_filepath": null, + "feature_counts_filepath": null, + "count_type": "raw", + "sample_id_colname": null, + "feature_id_colname": null, + "delim": null +} diff --git a/code/MOSuite/inst/extdata/json_args/defaults/diff_counts.json b/code/MOSuite/inst/extdata/json_args/defaults/diff_counts.json new file mode 100644 index 0000000..bc0c531 --- /dev/null +++ b/code/MOSuite/inst/extdata/json_args/defaults/diff_counts.json @@ -0,0 +1,18 @@ +{ + "moo_input_rds": "moo.rds", + "moo_output_rds": "moo.rds", + "count_type": "filt", + "sub_count_type": null, + "sample_id_colname": null, + "feature_id_colname": null, + "samples_to_include": null, + "covariates_colnames": null, + "contrast_colname": null, + "contrasts": null, + "input_in_log_counts": false, + "return_mean_and_sd": false, + "voom_normalization_method": "quantile", + "print_plots": true, + "save_plots": true, + "plots_subdir": "diff" +} diff --git a/code/MOSuite/inst/extdata/json_args/defaults/filter_counts.json b/code/MOSuite/inst/extdata/json_args/defaults/filter_counts.json new file mode 100644 index 0000000..1e6feff --- /dev/null +++ b/code/MOSuite/inst/extdata/json_args/defaults/filter_counts.json @@ -0,0 +1,37 @@ +{ + "moo_input_rds": "moo.rds", + "moo_output_rds": "moo.rds", + "count_type": "clean", + "feature_id_colname": null, + "sample_id_colname": null, + "group_colname": "Group", + "label_colname": null, + "samples_to_include": null, + "minimum_count_value_to_be_considered_nonzero": 8, + "minimum_number_of_samples_with_nonzero_counts_in_total": 7, + "minimum_number_of_samples_with_nonzero_counts_in_a_group": 3, + "use_cpm_counts_to_filter": true, + "use_group_based_filtering": false, + "principal_component_on_x_axis": 1, + "principal_component_on_y_axis": 2, + "legend_position_for_pca": "top", + "point_size_for_pca": 1, + "add_label_to_pca": true, + "label_font_size": 3, + "label_offset_y_": 2, + "label_offset_x_": 2, + "samples_to_rename": "", + "color_histogram_by_group": false, + "set_min_max_for_x_axis_for_histogram": false, + "minimum_for_x_axis_for_histogram": -1, + "maximum_for_x_axis_for_histogram": 1, + "legend_position_for_histogram": "top", + "legend_font_size_for_histogram": 10, + "number_of_histogram_legend_columns": 6, + "colors_for_plots": null, + "plot_corr_matrix_heatmap": true, + "print_plots": true, + "save_plots": true, + "interactive_plots": false, + "plots_subdir": "filt" +} diff --git a/code/MOSuite/inst/extdata/json_args/defaults/filter_diff.json b/code/MOSuite/inst/extdata/json_args/defaults/filter_diff.json new file mode 100644 index 0000000..d255743 --- /dev/null +++ b/code/MOSuite/inst/extdata/json_args/defaults/filter_diff.json @@ -0,0 +1,29 @@ +{ + "moo_input_rds": "moo.rds", + "moo_output_rds": "moo.rds", + "feature_id_colname": null, + "significance_column": "adjpval", + "significance_cutoff": 0.05, + "change_column": "logFC", + "change_cutoff": 1, + "filtering_mode": "any", + "include_estimates": ["FC", "logFC", "tstat", "pval", "adjpval"], + "round_estimates": true, + "rounding_decimal_for_percent_cells": 0, + "contrast_filter": "none", + "contrasts": null, + "groups": null, + "groups_filter": "none", + "label_font_size": 6, + "label_distance": 1, + "y_axis_expansion": 0.08, + "fill_colors": ["steelblue1", "whitesmoke"], + "pie_chart_in_3d": true, + "bar_width": 0.4, + "draw_bar_border": true, + "plot_type": "bar", + "plot_titles_fontsize": 12, + "print_plots": true, + "save_plots": true, + "plots_subdir": "diff/filt" +} diff --git a/code/MOSuite/inst/extdata/json_args/defaults/normalize_counts.json b/code/MOSuite/inst/extdata/json_args/defaults/normalize_counts.json new file mode 100644 index 0000000..50c0e32 --- /dev/null +++ b/code/MOSuite/inst/extdata/json_args/defaults/normalize_counts.json @@ -0,0 +1,35 @@ +{ + "moo_input_rds": "moo.rds", + "moo_output_rds": "moo.rds", + "count_type": "filt", + "norm_type": "voom", + "feature_id_colname": null, + "samples_to_include": null, + "sample_id_colname": null, + "group_colname": "Group", + "label_colname": null, + "input_in_log_counts": false, + "voom_normalization_method": "quantile", + "samples_to_rename": "", + "add_label_to_pca": true, + "principal_component_on_x_axis": 1, + "principal_component_on_y_axis": 2, + "legend_position_for_pca": "top", + "label_offset_x_": 2, + "label_offset_y_": 2, + "label_font_size": 3, + "point_size_for_pca": 8, + "color_histogram_by_group": true, + "set_min_max_for_x_axis_for_histogram": false, + "minimum_for_x_axis_for_histogram": -1, + "maximum_for_x_axis_for_histogram": 1, + "legend_font_size_for_histogram": 10, + "legend_position_for_histogram": "top", + "number_of_histogram_legend_columns": 6, + "plot_corr_matrix_heatmap": true, + "colors_for_plots": null, + "print_plots": true, + "save_plots": true, + "interactive_plots": false, + "plots_subdir": "norm" +} diff --git a/code/MOSuite/inst/extdata/json_args/defaults/plot_expr_heatmap.json b/code/MOSuite/inst/extdata/json_args/defaults/plot_expr_heatmap.json new file mode 100644 index 0000000..c421963 --- /dev/null +++ b/code/MOSuite/inst/extdata/json_args/defaults/plot_expr_heatmap.json @@ -0,0 +1,51 @@ +{ + "moo_input_rds": "moo.rds", + "moo_output_rds": "moo.rds", + "count_type": null, + "sub_count_type": null, + "sample_metadata": null, + "sample_id_colname": null, + "feature_id_colname": null, + "group_colname": "Group", + "label_colname": null, + "samples_to_include": null, + "color_values": ["#5954d6", "#e1562c", "#b80058", "#00c6f8", "#d163e6", "#00a76c", "#ff9287", "#008cf9", "#006e00", "#796880", "#FFA500", "#878500"], + "include_all_genes": false, + "filter_top_genes_by_variance": true, + "top_genes_by_variance_to_include": 500, + "specific_genes_to_include_in_heatmap": "None", + "cluster_genes": true, + "gene_distance_metric": "correlation", + "gene_clustering_method": "average", + "display_gene_dendrograms": true, + "display_gene_names": false, + "center_and_rescale_expression": true, + "cluster_samples": false, + "arrange_sample_columns": true, + "order_by_gene_expression": false, + "gene_to_order_columns": " ", + "gene_expression_order": "low_to_high", + "smpl_distance_metric": "correlation", + "smpl_clustering_method": "average", + "display_smpl_dendrograms": true, + "reorder_dendrogram": false, + "reorder_dendrogram_order": null, + "display_sample_names": true, + "group_columns": ["Group", "Replicate", "Batch"], + "assign_group_colors": false, + "assign_color_to_sample_groups": null, + "group_colors": ["#5954d6", "#e1562c", "#b80058", "#00c6f8", "#d163e6", "#00a76c", "#ff9287", "#008cf9", "#006e00", "#796880", "#FFA500", "#878500"], + "heatmap_color_scheme": "Default", + "autoscale_heatmap_color": true, + "set_min_heatmap_color": -2, + "set_max_heatmap_color": 2, + "aspect_ratio": "Auto", + "legend_font_size": 10, + "gene_name_font_size": 4, + "sample_name_font_size": 8, + "display_numbers": false, + "plot_filename": "expr_heatmap.png", + "print_plots": true, + "save_plots": true, + "plots_subdir": "heatmap" +} diff --git a/code/MOSuite/inst/extdata/json_args/defaults/plot_pca_2d.json b/code/MOSuite/inst/extdata/json_args/defaults/plot_pca_2d.json new file mode 100644 index 0000000..edada7f --- /dev/null +++ b/code/MOSuite/inst/extdata/json_args/defaults/plot_pca_2d.json @@ -0,0 +1,25 @@ +{ + "moo_input_rds": "moo.rds", + "moo_output_rds": "moo.rds", + "count_type": null, + "sub_count_type": null, + "sample_metadata": null, + "sample_id_colname": null, + "feature_id_colname": null, + "group_colname": "Group", + "label_colname": "Label", + "samples_to_rename": null, + "color_values": ["#5954d6", "#e1562c", "#b80058", "#00c6f8", "#d163e6", "#00a76c", "#ff9287", "#008cf9", "#006e00", "#796880", "#FFA500", "#878500"], + "principal_components": [1, 2], + "legend_position": "top", + "point_size": 1, + "add_label": true, + "label_font_size": 3, + "label_offset_x_": 2, + "label_offset_y_": 2, + "interactive_plots": false, + "plots_subdir": "pca", + "plot_filename": "pca_2D.png", + "print_plots": true, + "save_plots": true +} diff --git a/code/MOSuite/inst/extdata/json_args/defaults/plot_pca_3d.json b/code/MOSuite/inst/extdata/json_args/defaults/plot_pca_3d.json new file mode 100644 index 0000000..d8e342b --- /dev/null +++ b/code/MOSuite/inst/extdata/json_args/defaults/plot_pca_3d.json @@ -0,0 +1,21 @@ +{ + "moo_input_rds": "moo.rds", + "moo_output_rds": "moo.rds", + "count_type": null, + "sub_count_type": null, + "sample_metadata": null, + "feature_id_colname": null, + "sample_id_colname": null, + "samples_to_rename": null, + "group_colname": "Group", + "label_colname": "Label", + "principal_components": [1, 2, 3], + "point_size": 8, + "label_font_size": 24, + "color_values": ["#5954d6", "#e1562c", "#b80058", "#00c6f8", "#d163e6", "#00a76c", "#ff9287", "#008cf9", "#006e00", "#796880", "#FFA500", "#878500"], + "plot_title": "PCA 3D", + "plot_filename": "pca_3D.html", + "print_plots": true, + "save_plots": true, + "plots_subdir": "pca" +} diff --git a/code/MOSuite/inst/extdata/json_args/defaults/plot_venn_diagram.json b/code/MOSuite/inst/extdata/json_args/defaults/plot_venn_diagram.json new file mode 100644 index 0000000..10e4fb8 --- /dev/null +++ b/code/MOSuite/inst/extdata/json_args/defaults/plot_venn_diagram.json @@ -0,0 +1,35 @@ +{ + "moo_input_rds": "moo.rds", + "moo_output_rds": "moo.rds", + "feature_id_colname": null, + "contrasts_colname": "Contrast", + "select_contrasts": null, + "plot_type": "Venn diagram", + "intersection_ids": null, + "venn_force_unique": true, + "venn_numbers_format": "raw", + "venn_significant_digits": 2, + "venn_fill_colors": ["darkgoldenrod2", "darkolivegreen2", "mediumpurple3", "darkorange2", "lightgreen"], + "venn_fill_transparency": 0.2, + "venn_border_colors": "fill colors", + "venn_font_size_for_category_names": 3, + "venn_category_names_distance": null, + "venn_category_names_position": null, + "venn_font_size_for_counts": 6, + "venn_outer_margin": 0, + "intersections_order": "degree", + "display_empty_intersections": false, + "intersection_bar_color": "steelblue4", + "intersection_point_size": 2.2, + "intersection_line_width": 0.7, + "table_font_size": 0.7, + "table_content": "all intersections", + "graphics_device": ["function (filename = \"Rplot%03d.png\", width = 480, height = 480, ", " units = \"px\", pointsize = 12, bg = \"white\", res = NA, ..., ", " type = c(\"cairo\", \"cairo-png\", \"Xlib\", \"quartz\"), antialias) ", "{", " if (!is.character(filename) || length(filename) != 1L || ", " !nzchar(filename)) ", " stop(\"'filename' must be a non-empty character string\")", " if (!checkIntFormat(filename)) ", " stop(\"invalid 'filename'\")", " g <- .geometry(width, height, units, res)", " new <- list(...)", " if (missing(type)) ", " type <- getOption(\"bitmapType\")", " type <- match.arg(type)", " if (!missing(antialias)) ", " new$antialias <- match.arg(antialias, aa.cairo)", " d <- check.options(new, name.opt = \".X11.Options\", envir = .X11env)", " antialias <- match(d$antialias, aa.cairo)", " if (type == \"quartz\") {", " if (capabilities(\"aqua\")) {", " width <- g$width/ifelse(is.na(res), 72, res)", " height <- g$height/ifelse(is.na(res), 72, res)", " invisible(.External(C_Quartz, \"png\", path.expand(filename), ", " width, height, pointsize, d$family, d$antialias != ", " \"none\", \"\", bg, \"white\", if (is.na(res)) NULL else res))", " }", " else warning(\"type = \\\"quartz\\\" is unavailable. trying \\\"Xlib\\\"\")", " }", " else if (type == \"cairo\") {", " if (capabilities(\"cairo\")) {", " invisible(.External(C_devCairo, filename, 2L, g$width, ", " g$height, pointsize, bg, res, antialias, 100L, ", " d$family, 300, optionSymbolFont(d$symbolfamily)))", " }", " else warning(\"type = \\\"cairo\\\" is unavailable. trying \\\"Xlib\\\"\")", " }", " else if (type == \"cairo-png\") {", " if (capabilities(\"cairo\")) {", " invisible(.External(C_devCairo, filename, 5L, g$width, ", " g$height, pointsize, bg, res, antialias, 100L, ", " d$family, 300, optionSymbolFont(d$symbolfamily)))", " }", " else warning(\"type = \\\"cairo-png\\\" is unavailable. trying \\\"Xlib\\\"\")", " }", " else invisible(.External2(C_X11, paste0(\"png::\", filename), ", " g$width, g$height, pointsize, d$gamma, d$colortype, d$maxcubesize, ", " bg, bg, d$fonts, res, 0L, 0L, \"\", 0, 0, d$family, optionSymbolFont(d$symbolfamily)))", "}"], + "dpi": 300, + "image_width": 4000, + "image_height": 3000, + "plot_filename": "venn_diagram.png", + "print_plots": true, + "save_plots": true, + "plots_subdir": "diff" +} diff --git a/code/MOSuite/inst/extdata/json_args/defaults/plot_volcano_enhanced.json b/code/MOSuite/inst/extdata/json_args/defaults/plot_volcano_enhanced.json new file mode 100644 index 0000000..6185918 --- /dev/null +++ b/code/MOSuite/inst/extdata/json_args/defaults/plot_volcano_enhanced.json @@ -0,0 +1,33 @@ +{ + "moo_input_rds": "moo.rds", + "moo_output_rds": "moo.rds", + "feature_id_colname": null, + "signif_colname": ["B-A_adjpval", "B-C_adjpval"], + "signif_threshold": 0.05, + "change_colname": ["B-A_logFC", "B-C_logFC"], + "change_threshold": 1, + "value_to_sort_the_output_dataset": "p-value", + "num_features_to_label": 30, + "use_only_addition_labels": false, + "additional_labels": "", + "is_red": true, + "lab_size": 4, + "change_sig_name": "p-value", + "change_lfc_name": "log2FC", + "title": "Volcano Plots", + "use_custom_lab": false, + "ylim": 0, + "custom_xlim": "", + "xlim_additional": 0, + "ylim_additional": 0, + "axis_lab_size": 24, + "point_size": 2, + "image_width": 3000, + "image_height": 3000, + "dpi": 300, + "interactive_plots": false, + "print_plots": true, + "save_plots": true, + "plots_subdir": "diff", + "plot_filename": "volcano_enhanced.png" +} diff --git a/code/MOSuite/inst/extdata/json_args/defaults/plot_volcano_summary.json b/code/MOSuite/inst/extdata/json_args/defaults/plot_volcano_summary.json new file mode 100644 index 0000000..a7cf8ea --- /dev/null +++ b/code/MOSuite/inst/extdata/json_args/defaults/plot_volcano_summary.json @@ -0,0 +1,47 @@ +{ + "moo_input_rds": "moo.rds", + "moo_output_rds": "moo.rds", + "feature_id_colname": null, + "signif_colname": "pval", + "signif_threshold": 0.05, + "change_threshold": 1, + "value_to_sort_the_output_dataset": "t-statistic", + "num_features_to_label": 30, + "add_features": false, + "label_features": false, + "custom_gene_list": "", + "default_label_color": "black", + "custom_label_color": "green3", + "label_x_adj": 0.2, + "label_y_adj": 0.2, + "line_thickness": 0.5, + "label_font_size": 4, + "label_font_type": 1, + "displace_feature_labels": false, + "custom_gene_list_special_label_displacement": "", + "special_label_displacement_x_axis": 2, + "special_label_displacement_y_axis": 2, + "color_of_signif_threshold_line": "blue", + "color_of_non_significant_features": "black", + "color_of_logfold_change_threshold_line": "red", + "color_of_features_meeting_only_signif_threshold": "lightgoldenrod2", + "color_for_features_meeting_pvalue_and_foldchange_thresholds": "red", + "flip_vplot": false, + "use_default_x_axis_limit": true, + "x_axis_limit": 5, + "use_default_y_axis_limit": true, + "y_axis_limit": 10, + "point_size": 2, + "add_deg_columns": ["FC", "logFC", "tstat", "pval", "adjpval"], + "graphics_device": ["function (filename = \"Rplot%03d.png\", width = 480, height = 480, ", " units = \"px\", pointsize = 12, bg = \"white\", res = NA, ..., ", " type = c(\"cairo\", \"cairo-png\", \"Xlib\", \"quartz\"), antialias) ", "{", " if (!is.character(filename) || length(filename) != 1L || ", " !nzchar(filename)) ", " stop(\"'filename' must be a non-empty character string\")", " if (!checkIntFormat(filename)) ", " stop(\"invalid 'filename'\")", " g <- .geometry(width, height, units, res)", " new <- list(...)", " if (missing(type)) ", " type <- getOption(\"bitmapType\")", " type <- match.arg(type)", " if (!missing(antialias)) ", " new$antialias <- match.arg(antialias, aa.cairo)", " d <- check.options(new, name.opt = \".X11.Options\", envir = .X11env)", " antialias <- match(d$antialias, aa.cairo)", " if (type == \"quartz\") {", " if (capabilities(\"aqua\")) {", " width <- g$width/ifelse(is.na(res), 72, res)", " height <- g$height/ifelse(is.na(res), 72, res)", " invisible(.External(C_Quartz, \"png\", path.expand(filename), ", " width, height, pointsize, d$family, d$antialias != ", " \"none\", \"\", bg, \"white\", if (is.na(res)) NULL else res))", " }", " else warning(\"type = \\\"quartz\\\" is unavailable. trying \\\"Xlib\\\"\")", " }", " else if (type == \"cairo\") {", " if (capabilities(\"cairo\")) {", " invisible(.External(C_devCairo, filename, 2L, g$width, ", " g$height, pointsize, bg, res, antialias, 100L, ", " d$family, 300, optionSymbolFont(d$symbolfamily)))", " }", " else warning(\"type = \\\"cairo\\\" is unavailable. trying \\\"Xlib\\\"\")", " }", " else if (type == \"cairo-png\") {", " if (capabilities(\"cairo\")) {", " invisible(.External(C_devCairo, filename, 5L, g$width, ", " g$height, pointsize, bg, res, antialias, 100L, ", " d$family, 300, optionSymbolFont(d$symbolfamily)))", " }", " else warning(\"type = \\\"cairo-png\\\" is unavailable. trying \\\"Xlib\\\"\")", " }", " else invisible(.External2(C_X11, paste0(\"png::\", filename), ", " g$width, g$height, pointsize, d$gamma, d$colortype, d$maxcubesize, ", " bg, bg, d$fonts, res, 0L, 0L, \"\", 0, 0, d$family, optionSymbolFont(d$symbolfamily)))", "}"], + "image_width": 15, + "image_height": 15, + "dpi": 300, + "use_default_grid_layout": true, + "number_of_rows_in_grid_layout": 1, + "aspect_ratio": 0, + "plot_filename": "volcano_summary.png", + "print_plots": true, + "save_plots": true, + "plots_subdir": "diff" +} diff --git a/code/MOSuite/inst/extdata/json_args/defaults/write_multiOmicDataSet_properties.json b/code/MOSuite/inst/extdata/json_args/defaults/write_multiOmicDataSet_properties.json new file mode 100644 index 0000000..123f832 --- /dev/null +++ b/code/MOSuite/inst/extdata/json_args/defaults/write_multiOmicDataSet_properties.json @@ -0,0 +1,5 @@ +{ + "moo_input_rds": "moo.rds", + "moo_output_rds": "moo.rds", + "output_dir": "moo" +} diff --git a/code/MOSuite/inst/extdata/logo/create_logo.R b/code/MOSuite/inst/extdata/logo/create_logo.R new file mode 100644 index 0000000..ee0fc57 --- /dev/null +++ b/code/MOSuite/inst/extdata/logo/create_logo.R @@ -0,0 +1,213 @@ +#!/usr/bin/env Rscript +# Create hex logo for MOSuite package +# Design: Combine volcano plot + heatmap + +library(ggplot2) +library(hexSticker) +library(ggimage) +library(magick) +library(tidyverse) + +# Create directory if it doesn't exist + +set.seed(123) + +emoji_url <- "https://raw.githubusercontent.com/twitter/twemoji/master/assets/72x72/1f42e.png" +emoji_temp <- tempfile(fileext = ".png") +download.file(emoji_url, emoji_temp, quiet = TRUE, mode = "wb") + +# Convert to grayscale and apply transparency +emoji_gray <- magick::image_read(emoji_temp) |> + magick::image_quantize(colorspace = "gray") +emoji_gray_transparent <- magick::image_fx( + emoji_gray, + "0.3*u", + channel = "alpha" +) +magick::image_write(emoji_gray_transparent, emoji_temp) + +emoji_df <- data.frame( + x = 0.366, + y = 0.73, + image = emoji_temp +) + + +# ---- Volcano plot layer ---- + +load(here::here('data', 'nidap_deg_analysis.rda')) +volcano_data <- nidap_deg_analysis |> + rename(log2fc = `C-A_logFC`) |> + mutate(neg_log10_pval = -log10(`C-A_pval`)) + +fc_cut <- 1.0 +p_cut <- 2.5 + +volcano_data <- volcano_data |> + mutate( + regulation = case_when( + log2fc >= fc_cut & neg_log10_pval >= p_cut ~ "Upregulated", + log2fc <= -fc_cut & neg_log10_pval >= p_cut ~ "Downregulated", + neg_log10_pval >= p_cut ~ "Significant", + .default = "Not significant" + ), + x = scales::rescale(log2fc, to = c(0.12, 0.88)), + y = scales::rescale(neg_log10_pval, to = c(0.18, 0.94)), + color = case_when( + regulation == "Upregulated" ~ "#4e9db5", + regulation == "Downregulated" ~ "#ecba4c", + regulation == "Significant" ~ "#528230", + regulation == "Not significant" ~ "#999999", + .default = NA_character_ + ) + ) + +# ---- Heatmap layer ---- +rows <- paste0("G", sprintf("%02d", 1:12)) +cols <- paste0("S", sprintf("%02d", 1:10)) + +base_matrix <- matrix(rnorm(12 * 10, mean = 0, sd = 0.5), nrow = 12, ncol = 10) +base_matrix[1:4, 1:5] <- base_matrix[1:4, 1:5] + 2.0 # up cluster +base_matrix[9:12, 6:10] <- base_matrix[9:12, 6:10] - 2.0 # down cluster +base_matrix[5:8, 4:7] <- base_matrix[5:8, 4:7] + 1.0 # moderate cluster + +heatmap_df <- expand.grid(Row = rows, Col = cols) |> + mutate( + Value = as.vector(base_matrix), + Value = scales::rescale(Value, to = c(-2, 2)), + x = scales::rescale( + as.numeric(factor(Col, levels = cols)), + to = c(0.10, 0.90) + ), + y = scales::rescale( + as.numeric(factor(Row, levels = rows)), + to = c(0.16, 0.96) + ) + ) + +heat_colors <- c("#4e9db5", "#F7F7F7", "#ecba4c") +tile_width <- (0.90 - 0.10) / length(cols) +tile_height <- (0.96 - 0.16) / length(rows) + +# ---- Combined plot ---- +# Heatmap as background, volcano points as foreground +p <- ggplot() + + geom_tile( + data = heatmap_df, + aes(x = x, y = y, fill = Value), + width = tile_width, + height = tile_height, + color = "#D0D0D0", + linewidth = 0.2, + alpha = 0.5, + show.legend = FALSE + ) + + scale_fill_gradient2( + low = heat_colors[1], + mid = heat_colors[2], + high = heat_colors[3], + midpoint = 0, + guide = "none" + ) + + # Volcano points on top + geom_point( + data = volcano_data, + aes(x = x, y = y, color = color), + size = 2.0, + alpha = 0.5, + shape = 16, + show.legend = FALSE + ) + + annotate( + "text", + x = 0.5, + y = 0.725, + label = "MOSuite", + size = 16, + fontface = "bold", + family = "sans", + color = "#296b7f" + ) + + ggimage::geom_image( + # emoji + data = emoji_df, + aes(x = 0.33, y = 0.725, image = image), + size = 0.08, + inherit.aes = FALSE + ) + + scale_color_identity() + + coord_fixed(xlim = c(0, 1), ylim = c(0, 1), expand = FALSE) + + theme_void() + + theme( + plot.background = element_rect(fill = "#FFF", color = NA), + plot.margin = margin(0, 0, 0, 0) + ) +print(p) + +ggsave( + here::here('inst', 'extdata', 'logo', 'mosuite_logo_with_text.png'), + plot = p, + dpi = 300, + width = 3, + height = 3 +) + +# background only +p_background <- ggplot() + + geom_tile( + data = heatmap_df, + aes(x = x, y = y, fill = Value), + width = tile_width, + height = tile_height, + color = "#D0D0D0", + linewidth = 0.2, + alpha = 0.8, + show.legend = FALSE + ) + + scale_fill_gradient2( + low = heat_colors[1], + mid = heat_colors[2], + high = heat_colors[3], + midpoint = 0, + guide = "none" + ) + + # Volcano points on top + geom_point( + data = volcano_data, + aes(x = x, y = y, color = color), + size = 2.0, + alpha = 0.8, + shape = 16, + show.legend = FALSE + ) + + ggimage::geom_image( + # emoji + data = emoji_df, + aes(x = 0.33, y = 0.725, image = image), + size = 0.08, + inherit.aes = FALSE + ) + + scale_color_identity() + + coord_fixed(xlim = c(0, 1), ylim = c(0, 1), expand = FALSE) + + theme_void() + + theme( + plot.background = element_rect(fill = "#FFF", color = NA), + plot.margin = margin(0, 0, 0, 0) + ) +print(p_background) +ggsave( + here::here('inst', 'extdata', 'logo', 'mosuite_logo_background.png'), + plot = p_background, + dpi = 300, + width = 3, + height = 3 +) + +# need to run this line interactively for it to actually overwrite the logo file +usethis::use_logo(here::here( + 'inst', + 'extdata', + 'logo', + 'mosuite_logo_background.png' +)) +pkgdown::build_favicons(overwrite = TRUE) diff --git a/code/MOSuite/inst/extdata/logo/mosuite_logo_background.png b/code/MOSuite/inst/extdata/logo/mosuite_logo_background.png new file mode 100644 index 0000000..eb0645e Binary files /dev/null and b/code/MOSuite/inst/extdata/logo/mosuite_logo_background.png differ diff --git a/code/MOSuite/inst/extdata/logo/mosuite_logo_with_text.png b/code/MOSuite/inst/extdata/logo/mosuite_logo_with_text.png new file mode 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index 0000000..022e127 Binary files /dev/null and b/code/MOSuite/inst/extdata/sample_metadata.tsv.gz differ diff --git a/code/MOSuite/man/MOSuite-package.Rd b/code/MOSuite/man/MOSuite-package.Rd new file mode 100644 index 0000000..f9afbde --- /dev/null +++ b/code/MOSuite/man/MOSuite-package.Rd @@ -0,0 +1,43 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/MOSuite-package.R +\docType{package} +\name{MOSuite-package} +\alias{MOSuite} +\alias{MOSuite-package} +\title{MOSuite: R package for downstream multi-omics analysis} +\description{ +Designed for differential \href{https://github.com/CCBR/RENEE}{RNA-seq} analysis +or any data represented in a counts table. +} +\details{ +See the website for more information, documentation, and examples: +\url{https://ccbr.github.io/MOSuite} +} +\seealso{ +Useful links: +\itemize{ + \item \url{https://github.com/CCBR/MOSuite} + \item \url{https://ccbr.github.io/MOSuite/} + \item Report bugs at \url{https://github.com/CCBR/MOSuite/issues} +} + +} +\author{ +\strong{Maintainer}: Kelly Sovacool \email{kelly.sovacool@nih.gov} (\href{https://orcid.org/0000-0003-3283-829X}{ORCID}) + +Authors: +\itemize{ + \item Kelly Sovacool \email{kelly.sovacool@nih.gov} (\href{https://orcid.org/0000-0003-3283-829X}{ORCID}) + \item Philip Homan \email{philip.homan@nih.gov} + \item Vishal Koparde \email{vishal.koparde@nih.gov} (\href{https://orcid.org/0000-0001-8978-8495}{ORCID}) + \item Samantha Chill \email{samantha.chill@nih.gov} (\href{https://orcid.org/0000-0002-8734-9875}{ORCID}) +} + +Other contributors: +\itemize{ + \item T. Joshua Meyer \email{thomas.meyer@nih.gov} [contributor] + \item CCR Collaborative Bioinformatics Resource [copyright holder] +} + +} +\keyword{internal} diff --git a/code/MOSuite/man/abort_packages_not_installed.Rd b/code/MOSuite/man/abort_packages_not_installed.Rd new file mode 100644 index 0000000..929885a --- /dev/null +++ b/code/MOSuite/man/abort_packages_not_installed.Rd @@ -0,0 +1,23 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/utils.R +\name{abort_packages_not_installed} +\alias{abort_packages_not_installed} +\title{Throw error if required packages are not installed.} +\usage{ +abort_packages_not_installed(...) +} +\arguments{ +\item{...}{names of packages to check} +} +\description{ +Reports which packages need to be installed and the parent function name. +See +https://stackoverflow.com/questions/15595478/how-to-get-the-name-of-the-calling-function-inside-the-called-routine +} +\examples{ +\dontrun{ +abort_packages_not_installed("base") +abort_packages_not_installed("not-a-package-name", "caret", "dplyr", "non_package") +} +} +\keyword{internal} diff --git a/code/MOSuite/man/aggregate_duplicate_gene_names.Rd b/code/MOSuite/man/aggregate_duplicate_gene_names.Rd new file mode 100644 index 0000000..368d64b --- /dev/null +++ b/code/MOSuite/man/aggregate_duplicate_gene_names.Rd @@ -0,0 +1,46 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/clean.R +\name{aggregate_duplicate_gene_names} +\alias{aggregate_duplicate_gene_names} +\title{Aggregate duplicate gene names} +\usage{ +aggregate_duplicate_gene_names( + counts_dat, + gene_name_column_to_use_for_collapsing_duplicates, + aggregate_rows_with_duplicate_gene_names, + split_gene_name +) +} +\arguments{ +\item{counts_dat}{dataframe with raw counts data} + +\item{gene_name_column_to_use_for_collapsing_duplicates}{Select the column +with Feature IDs to use as grouping elements to collapse the counts matrix. +The log output will list the columns available to identify duplicate row +IDs in order to aggregate information. +If left blank your "Feature ID" Column will be used to Aggregate Rows. If +"Feature ID" column can be split into multiple IDs the non Ensembl ID name +will be used to aggregate duplicate IDs. If "Feature ID" column does not +contain Ensembl IDs the split Feature IDs will be named 'Feature_id_1' and +'Feature_id_2'. For this case an error will occur and you will have +to manually enter the Column ID for this field.} + +\item{aggregate_rows_with_duplicate_gene_names}{If a Feature ID (from the +"Cleanup Column Names" parameter above) is found to be duplicated on +multiple rows of the raw counts, the Log will report these Feature IDs. +Using the default behavior (\code{TRUE}), the counts for all rows with a +duplicate Feature IDs are aggregated into a single row. Counts are summed +across duplicate Feature ID rows within each sample. Additional identifier +columns, if present (e.g. Ensembl IDs), will be preserved and multiple +matching identifiers in such additional columns will appear as +comma-separated values in an aggregated row.} + +\item{split_gene_name}{If \code{TRUE}, split the gene name column by any of these special characters: \verb{,|_-:}} +} +\value{ +data frame with columns separated if possible +} +\description{ +Aggregate duplicate gene names +} +\keyword{internal} diff --git a/code/MOSuite/man/as_integer_df.Rd b/code/MOSuite/man/as_integer_df.Rd new file mode 100644 index 0000000..9bf4fce --- /dev/null +++ b/code/MOSuite/man/as_integer_df.Rd @@ -0,0 +1,23 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/counts.R +\name{as_integer_df} +\alias{as_integer_df} +\title{Convert all numeric columns in a dataframe to integers} +\usage{ +as_integer_df(counts_tbl) +} +\arguments{ +\item{counts_tbl}{data frame with numeric columns} +} +\value{ +data frame with any numeric columns as integers +} +\description{ +Round doubles to integers and convert to integer type +} +\examples{ +\dontrun{ +data.frame(a = c(0, 0.1, 2.3, 5L, 6.9)) |> as_integer_df() +} +} +\keyword{internal} diff --git a/code/MOSuite/man/batch_correct_counts.Rd b/code/MOSuite/man/batch_correct_counts.Rd new file mode 100644 index 0000000..9be8aa8 --- /dev/null +++ b/code/MOSuite/man/batch_correct_counts.Rd @@ -0,0 +1,116 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/batch-correction.R +\name{batch_correct_counts} +\alias{batch_correct_counts} +\title{Perform batch correction} +\usage{ +batch_correct_counts( + moo, + count_type = "norm", + sub_count_type = "voom", + sample_id_colname = NULL, + feature_id_colname = NULL, + samples_to_include = NULL, + covariates_colnames = "Group", + batch_colname = "Batch", + label_colname = NULL, + colors_for_plots = NULL, + print_plots = options::opt("print_plots"), + save_plots = options::opt("save_plots"), + plots_subdir = "batch" +) +} +\arguments{ +\item{moo}{multiOmicDataSet object (see \code{create_multiOmicDataSet_from_dataframes()})} + +\item{count_type}{the type of counts to use -- must be a name in the counts slot (\code{moo@counts})} + +\item{sub_count_type}{if \code{count_type} is a list, specify the sub count type within the list. (Default: \code{"voom"})} + +\item{sample_id_colname}{The column from the sample metadata containing the sample names. The names in this column +must exactly match the names used as the sample column names of your input Counts Matrix. (Default: \code{NULL} - first +column in the sample metadata will be used.)} + +\item{feature_id_colname}{The column from the counts data containing the Feature IDs (Usually Gene or Protein ID). +This is usually the first column of your input Counts Matrix. Only columns of Text type from your input Counts +Matrix will be available to select for this parameter. (Default: \code{NULL} - first column in the counts matrix will be +used.)} + +\item{samples_to_include}{Which samples would you like to include? Usually, you will choose all sample columns, or +you could choose to remove certain samples. Samples excluded here will be removed in this step and from further +analysis downstream of this step. (Default: \code{NULL} - all sample IDs in \code{moo@sample_meta} will be used.)} + +\item{covariates_colnames}{The column name(s) from the sample metadata +containing variable(s) of interest, such as phenotype. +Most commonly this will be the same column selected for your Groups Column. +Some experimental designs may require that you add additional covariate columns here. +Do not include the \code{batch_colname} here.} + +\item{batch_colname}{The column from the sample metadata containing the batch information. +Samples extracted, prepared, or sequenced at separate times or using separate materials/staff/equipment +may belong to different batches. +Not all data sets have batches, in which case you do not need batch correction. +If your data set has no batches, you can provide a batch column with the same +value in every row to skip batch correction (alternatively, simply do not run this function).} + +\item{label_colname}{The column from the sample metadata containing the sample labels as you wish them to appear in +the plots produced by this template. This can be the same Sample Names Column. However, you may desire different +labels to display on your figure (e.g. shorter labels are sometimes preferred on plots). In that case, select the +column with your preferred Labels here. The selected column should contain unique names for each sample. (Default: +\code{NULL} -- \code{sample_id_colname} will be used.)} + +\item{colors_for_plots}{Colors for the PCA and histogram will be picked, in order, from this list. +Colors must either be names in \code{grDevices::colors()} or valid hex codes.} + +\item{print_plots}{Whether to print plots during analysis (Defaults to \code{FALSE}, overwritable using option 'moo_print_plots' or environment variable 'MOO_PRINT_PLOTS')} + +\item{save_plots}{Whether to save plots to files during analysis (Defaults to \code{TRUE}, overwritable using option 'moo_save_plots' or environment variable 'MOO_SAVE_PLOTS')} + +\item{plots_subdir}{subdirectory in \verb{figures/} where plots will be saved if \code{save_plots} is \code{TRUE}} +} +\value{ +\code{multiOmicDataSet} with batch-corrected counts +} +\description{ +Perform batch correction using sva::ComBat() +} +\examples{ +moo <- multiOmicDataSet( + sample_metadata = as.data.frame(nidap_sample_metadata), + anno_dat = data.frame(), + counts_lst = list( + "raw" = as.data.frame(nidap_raw_counts), + "clean" = as.data.frame(nidap_clean_raw_counts), + "filt" = as.data.frame(nidap_filtered_counts), + "norm" = list( + "voom" = as.data.frame(nidap_norm_counts) + ) + ) +) |> + batch_correct_counts( + count_type = "norm", + sub_count_type = "voom", + covariates_colnames = "Group", + batch_colname = "Batch", + label_colname = "Label" + ) + +head(moo@counts[["batch"]]) + +} +\seealso{ +Other moo methods: +\code{\link[=clean_raw_counts]{clean_raw_counts()}}, +\code{\link[=diff_counts]{diff_counts()}}, +\code{\link[=filter_counts]{filter_counts()}}, +\code{\link[=filter_diff]{filter_diff()}}, +\code{\link[=normalize_counts]{normalize_counts()}}, +\code{\link[=plot_corr_heatmap]{plot_corr_heatmap()}}, +\code{\link[=plot_expr_heatmap]{plot_expr_heatmap()}}, +\code{\link[=plot_histogram]{plot_histogram()}}, +\code{\link[=plot_pca]{plot_pca()}}, +\code{\link[=plot_read_depth]{plot_read_depth()}}, +\code{\link[=run_deseq2]{run_deseq2()}}, +\code{\link[=set_color_pal]{set_color_pal()}} +} +\concept{moo methods} diff --git a/code/MOSuite/man/bind_dfs_long.Rd b/code/MOSuite/man/bind_dfs_long.Rd new file mode 100644 index 0000000..661d9b1 --- /dev/null +++ b/code/MOSuite/man/bind_dfs_long.Rd @@ -0,0 +1,29 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/utils.R +\name{bind_dfs_long} +\alias{bind_dfs_long} +\title{Bind dataframes in named list to long dataframe} +\usage{ +bind_dfs_long(df_list, outcolname = contrast) +} +\arguments{ +\item{df_list}{named list of dataframes} + +\item{outcolname}{column name in output dataframe for the names from the named list} +} +\value{ +long dataframe with new column \code{outcolname} from named list +} +\description{ +The dataframes must have all of the same columns +} +\examples{ + +dfs <- list( + "a_vs_b" = data.frame(id = c("a1", "b2", "c3"), score = runif(3)), + "b_vs_c" = data.frame(id = c("a1", "b2", "c3"), score = rnorm(3)) +) +dfs |> bind_dfs_long() + +} +\keyword{utilities} diff --git a/code/MOSuite/man/calc_cpm.Rd b/code/MOSuite/man/calc_cpm.Rd new file mode 100644 index 0000000..0c589da --- /dev/null +++ b/code/MOSuite/man/calc_cpm.Rd @@ -0,0 +1,31 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/counts.R +\name{calc_cpm} +\alias{calc_cpm} +\title{Calculate counts-per-million (CPM) on raw counts in a multiOmicDataSet} +\usage{ +calc_cpm(moo, ...) +} +\arguments{ +\item{moo}{multiOmicDataSet object} + +\item{...}{additional arguments to pass to edgeR::cpm()} +} +\value{ +multiOmicDataSet with cpm-transformed counts +} +\description{ +Calculate counts-per-million (CPM) on raw counts in a multiOmicDataSet +} +\examples{ +sample_meta <- data.frame( + sample_id = c("KO_S3", "KO_S4", "WT_S1", "WT_S2"), + condition = factor( + c("knockout", "knockout", "wildtype", "wildtype"), + levels = c("wildtype", "knockout") + ) +) +moo <- create_multiOmicDataSet_from_dataframes(sample_meta, gene_counts) |> + calc_cpm() +head(moo@counts$cpm) +} diff --git a/code/MOSuite/man/calc_cpm_df.Rd b/code/MOSuite/man/calc_cpm_df.Rd new file mode 100644 index 0000000..440e0f7 --- /dev/null +++ b/code/MOSuite/man/calc_cpm_df.Rd @@ -0,0 +1,23 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/counts.R +\name{calc_cpm_df} +\alias{calc_cpm_df} +\title{Calculate CPM on a data frame} +\usage{ +calc_cpm_df(dat, feature_id_colname = "gene_id", ...) +} +\arguments{ +\item{dat}{data frame of counts with a gene column} + +\item{feature_id_colname}{name of the column in \code{counts_dat} that contains feature/gene IDs. (Default: \code{NULL} - first +column in the count data will be used.)} + +\item{...}{additional arguments to pass to edger::cpm()} +} +\value{ +cpm-transformed counts as a data frame +} +\description{ +Calculate CPM on a data frame +} +\keyword{internal} diff --git a/code/MOSuite/man/calc_pca.Rd b/code/MOSuite/man/calc_pca.Rd new file mode 100644 index 0000000..c88960b --- /dev/null +++ b/code/MOSuite/man/calc_pca.Rd @@ -0,0 +1,43 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/plot_pca.R +\name{calc_pca} +\alias{calc_pca} +\title{Perform principal components analysis} +\usage{ +calc_pca( + counts_dat, + sample_metadata, + sample_id_colname = NULL, + feature_id_colname = NULL +) +} +\arguments{ +\item{counts_dat}{data frame of feature counts (e.g. from the counts slot of a \code{multiOmicDataSet}).} + +\item{sample_metadata}{sample metadata as a data frame or tibble.} + +\item{sample_id_colname}{The column from the sample metadata containing the sample names. The names in this column +must exactly match the names used as the sample column names of your input Counts Matrix. (Default: \code{NULL} - first +column in the sample metadata will be used.)} + +\item{feature_id_colname}{The column from the counts dataa containing the Feature IDs (Usually Gene or Protein ID). +This is usually the first column of your input Counts Matrix. Only columns of Text type from your input Counts +Matrix will be available to select for this parameter. (Default: \code{NULL} - first column in the counts matrix will be +used.)} +} +\value{ +data frame with statistics for each principal component +} +\description{ +Perform principal components analysis +} +\examples{ +calc_pca(nidap_raw_counts, nidap_sample_metadata) |> head() +} +\seealso{ +Other PCA functions: +\code{\link[=plot_pca]{plot_pca()}}, +\code{\link[=plot_pca_2d]{plot_pca_2d()}}, +\code{\link[=plot_pca_3d]{plot_pca_3d()}} +} +\concept{PCA functions} diff --git a/code/MOSuite/man/check_packages_installed.Rd b/code/MOSuite/man/check_packages_installed.Rd new file mode 100644 index 0000000..96e5a77 --- /dev/null +++ b/code/MOSuite/man/check_packages_installed.Rd @@ -0,0 +1,25 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/utils.R +\name{check_packages_installed} +\alias{check_packages_installed} +\title{Check whether package(s) are installed} +\usage{ +check_packages_installed(...) +} +\arguments{ +\item{...}{names of packages to check} +} +\value{ +named vector with status of each packages; installed (\code{TRUE}) or not (\code{FALSE}) +} +\description{ +Check whether package(s) are installed +} +\examples{ +\dontrun{ +check_packages_installed("base") +check_packages_installed("not-a-package-name") +all(check_packages_installed("parallel", "doFuture")) +} +} +\keyword{internal} diff --git a/code/MOSuite/man/clean_raw_counts.Rd b/code/MOSuite/man/clean_raw_counts.Rd new file mode 100644 index 0000000..f4f580d --- /dev/null +++ b/code/MOSuite/man/clean_raw_counts.Rd @@ -0,0 +1,112 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/clean.R +\name{clean_raw_counts} +\alias{clean_raw_counts} +\title{Clean Raw Counts} +\usage{ +clean_raw_counts( + moo, + count_type = "raw", + sample_id_colname = NULL, + feature_id_colname = NULL, + samples_to_rename = "", + cleanup_column_names = TRUE, + split_gene_name = TRUE, + aggregate_rows_with_duplicate_gene_names = TRUE, + gene_name_column_to_use_for_collapsing_duplicates = "", + print_plots = options::opt("print_plots"), + save_plots = options::opt("save_plots"), + plots_subdir = "clean" +) +} +\arguments{ +\item{moo}{multiOmicDataSet object (see \code{create_multiOmicDataSet_from_dataframes()})} + +\item{count_type}{the type of counts to use -- must be a name in the counts slot (\code{moo@counts})} + +\item{sample_id_colname}{The column from the sample metadata containing the sample names. The names in this column +must exactly match the names used as the sample column names of your input Counts Matrix. (Default: \code{NULL} - first +column in the sample metadata will be used.)} + +\item{feature_id_colname}{The column from the counts data containing the Feature IDs (Usually Gene or Protein ID). +This is usually the first column of your input Counts Matrix. Only columns of Text type from your input Counts +Matrix will be available to select for this parameter. (Default: \code{NULL} - first column in the counts matrix will be +used.)} + +\item{samples_to_rename}{If you do not have a Plot Labels Column in your sample metadata table, you can use this +parameter to rename samples manually for display on the PCA plot. Use "Add item" to add each additional sample for +renaming. Use the following format to describe which old name (in your sample metadata table) you want to rename to +which new name: old_name: new_name} + +\item{cleanup_column_names}{Invalid raw counts column names can cause errors +in the downstream analysis. If this is \code{TRUE}, any invalid column names +will be automatically altered to a correct format. These format changes +will include adding an "X" as the first character in any column name that +began with a numeral and replacing some special characters ("-,:. ") with +underscores ("_"). Invalid sample names and any changes made will be +detailed.} + +\item{split_gene_name}{If \code{TRUE}, split the gene name column by any of these special characters: \verb{,|_-:}} + +\item{aggregate_rows_with_duplicate_gene_names}{If a Feature ID (from the +"Cleanup Column Names" parameter above) is found to be duplicated on +multiple rows of the raw counts, the Log will report these Feature IDs. +Using the default behavior (\code{TRUE}), the counts for all rows with a +duplicate Feature IDs are aggregated into a single row. Counts are summed +across duplicate Feature ID rows within each sample. Additional identifier +columns, if present (e.g. Ensembl IDs), will be preserved and multiple +matching identifiers in such additional columns will appear as +comma-separated values in an aggregated row.} + +\item{gene_name_column_to_use_for_collapsing_duplicates}{Select the column +with Feature IDs to use as grouping elements to collapse the counts matrix. +The log output will list the columns available to identify duplicate row +IDs in order to aggregate information. +If left blank your "Feature ID" Column will be used to Aggregate Rows. If +"Feature ID" column can be split into multiple IDs the non Ensembl ID name +will be used to aggregate duplicate IDs. If "Feature ID" column does not +contain Ensembl IDs the split Feature IDs will be named 'Feature_id_1' and +'Feature_id_2'. For this case an error will occur and you will have +to manually enter the Column ID for this field.} + +\item{print_plots}{Whether to print plots during analysis (Defaults to \code{FALSE}, overwritable using option 'moo_print_plots' or environment variable 'MOO_PRINT_PLOTS')} + +\item{save_plots}{Whether to save plots to files during analysis (Defaults to \code{TRUE}, overwritable using option 'moo_save_plots' or environment variable 'MOO_SAVE_PLOTS')} + +\item{plots_subdir}{subdirectory in \verb{figures/} where plots will be saved if \code{save_plots} is \code{TRUE}} +} +\value{ +\code{multiOmicDataSet} with cleaned counts +} +\description{ +This function checks the input raw counts matrix for common formatting problems with feature identifiers and sample +names. If feature IDs contain multiple IDs separated by special characters (| - , or space) they will be split into +multiple columns. If duplicate feature IDs are detected the counts are summed across duplicate feature ID rows +within each sample. Invalid sample names will also be reported and can be automatically +corrected. If your sample names are corrected here, be sure to make equivalent changes to your metadata table. +} +\examples{ +moo <- create_multiOmicDataSet_from_dataframes( + as.data.frame(nidap_sample_metadata), + as.data.frame(nidap_raw_counts), + sample_id_colname = "Sample", +) |> + clean_raw_counts(sample_id_colname = "Sample", feature_id_colname = "GeneName") +head(moo@counts$clean) +} +\seealso{ +Other moo methods: +\code{\link[=batch_correct_counts]{batch_correct_counts()}}, +\code{\link[=diff_counts]{diff_counts()}}, +\code{\link[=filter_counts]{filter_counts()}}, +\code{\link[=filter_diff]{filter_diff()}}, +\code{\link[=normalize_counts]{normalize_counts()}}, +\code{\link[=plot_corr_heatmap]{plot_corr_heatmap()}}, +\code{\link[=plot_expr_heatmap]{plot_expr_heatmap()}}, +\code{\link[=plot_histogram]{plot_histogram()}}, +\code{\link[=plot_pca]{plot_pca()}}, +\code{\link[=plot_read_depth]{plot_read_depth()}}, +\code{\link[=run_deseq2]{run_deseq2()}}, +\code{\link[=set_color_pal]{set_color_pal()}} +} +\concept{moo methods} diff --git a/code/MOSuite/man/cli_exec.Rd b/code/MOSuite/man/cli_exec.Rd new file mode 100644 index 0000000..5b4e011 --- /dev/null +++ b/code/MOSuite/man/cli_exec.Rd @@ -0,0 +1,12 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/cli.R +\name{cli_exec} +\alias{cli_exec} +\title{Execute MOSuite from the CLI} +\usage{ +cli_exec(clargs = commandArgs(trailingOnly = TRUE)) +} +\description{ +Execute MOSuite from the CLI +} +\keyword{internal} diff --git a/code/MOSuite/man/cli_from_json.Rd b/code/MOSuite/man/cli_from_json.Rd new file mode 100644 index 0000000..c608dcb --- /dev/null +++ b/code/MOSuite/man/cli_from_json.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/cli.R +\name{cli_from_json} +\alias{cli_from_json} +\title{Call an MOSuite function with arguments specified in a json file} +\usage{ +cli_from_json(method, json, debug = FALSE) +} +\arguments{ +\item{method}{function in MOSuite to call} + +\item{json}{path to a JSON file containing arguments for the function. +Additionally, the JSON can contain the following keys: +\itemize{ +\item \code{moo_input_rds} - filepath to an existing MultiOmicsDataset object in RDS format. +This is required if the MOSuite function contains \code{moo} as an argument. +\item \code{moo_output_rds} - filepath to write the result to. +}} + +\item{debug}{when TRUE, do not call the command, just return the expression.} +} +\value{ +invisible returns the function call +} +\description{ +Call an MOSuite function with arguments specified in a json file +} +\keyword{internal} diff --git a/code/MOSuite/man/counts_dat_to_matrix.Rd b/code/MOSuite/man/counts_dat_to_matrix.Rd new file mode 100644 index 0000000..7976d80 --- /dev/null +++ b/code/MOSuite/man/counts_dat_to_matrix.Rd @@ -0,0 +1,26 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/counts.R +\name{counts_dat_to_matrix} +\alias{counts_dat_to_matrix} +\title{Convert a data frame of gene counts to a matrix} +\usage{ +counts_dat_to_matrix(counts_tbl, feature_id_colname = NULL) +} +\arguments{ +\item{counts_tbl}{expected feature counts as a dataframe or tibble, with all columns except \code{feature_id_colname}} + +\item{feature_id_colname}{name of the column in \code{counts_dat} that contains feature/gene IDs. (Default: \code{NULL} - first +column in the count data will be used.)} +} +\value{ +matrix of gene counts with rows as gene IDs +} +\description{ +Convert a data frame of gene counts to a matrix +} +\examples{ +\dontrun{ +counts_dat_to_matrix(head(gene_counts)) +} +} +\keyword{internal} diff --git a/code/MOSuite/man/create_multiOmicDataSet_from_dataframes.Rd b/code/MOSuite/man/create_multiOmicDataSet_from_dataframes.Rd new file mode 100644 index 0000000..2b41357 --- /dev/null +++ b/code/MOSuite/man/create_multiOmicDataSet_from_dataframes.Rd @@ -0,0 +1,63 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/0_mo-class.R +\name{create_multiOmicDataSet_from_dataframes} +\alias{create_multiOmicDataSet_from_dataframes} +\title{Construct a multiOmicDataSet object from data frames} +\usage{ +create_multiOmicDataSet_from_dataframes( + sample_metadata, + counts_dat, + sample_id_colname = NULL, + feature_id_colname = NULL, + count_type = "raw" +) +} +\arguments{ +\item{sample_metadata}{sample metadata as a data frame or tibble. The first column is assumed to contain the sample +IDs which must correspond to column names in the raw counts.} + +\item{counts_dat}{data frame of feature counts (e.g. expected feature counts from RSEM).} + +\item{sample_id_colname}{name of the column in \code{sample_metadata} that contains the sample IDs. (Default: \code{NULL} - +first column in the sample metadata will be used.)} + +\item{feature_id_colname}{name of the column in \code{counts_dat} that contains feature/gene IDs. (Default: \code{NULL} - first +column in the count data will be used.)} + +\item{count_type}{type to assign the values of \code{counts_dat} to in the \code{counts} slot} +} +\value{ +\link{multiOmicDataSet} object +} +\description{ +Construct a multiOmicDataSet object from data frames +} +\examples{ +sample_meta <- data.frame( + sample_id = c("KO_S3", "KO_S4", "WT_S1", "WT_S2"), + condition = factor( + c("knockout", "knockout", "wildtype", "wildtype"), + levels = c("wildtype", "knockout") + ) +) +moo <- create_multiOmicDataSet_from_dataframes(sample_meta, gene_counts) +head(moo@sample_meta) +head(moo@counts$raw) +head(moo@annotation) + +sample_meta_nidap <- readr::read_csv(system.file("extdata", "nidap", + "Sample_Metadata_Bulk_RNA-seq_Training_Dataset_CCBR.csv.gz", + package = "MOSuite" +)) +raw_counts_nidap <- readr::read_csv(system.file("extdata", "nidap", "Raw_Counts.csv.gz", + package = "MOSuite" +)) +moo_nidap <- create_multiOmicDataSet_from_dataframes(sample_meta_nidap, raw_counts_nidap) + +} +\seealso{ +Other moo constructors: +\code{\link[=create_multiOmicDataSet_from_files]{create_multiOmicDataSet_from_files()}}, +\code{\link[=multiOmicDataSet]{multiOmicDataSet()}} +} +\concept{moo constructors} diff --git a/code/MOSuite/man/create_multiOmicDataSet_from_files.Rd b/code/MOSuite/man/create_multiOmicDataSet_from_files.Rd new file mode 100644 index 0000000..b931f40 --- /dev/null +++ b/code/MOSuite/man/create_multiOmicDataSet_from_files.Rd @@ -0,0 +1,71 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/0_mo-class.R +\name{create_multiOmicDataSet_from_files} +\alias{create_multiOmicDataSet_from_files} +\title{Construct a multiOmicDataSet object from text files (e.g. TSV, CSV).} +\usage{ +create_multiOmicDataSet_from_files( + sample_meta_filepath, + feature_counts_filepath, + count_type = "raw", + sample_id_colname = NULL, + feature_id_colname = NULL, + delim = NULL, + ... +) +} +\arguments{ +\item{sample_meta_filepath}{path to text file with sample IDs and metadata for differential analysis.} + +\item{feature_counts_filepath}{path to text file of expected feature counts (e.g. gene counts from RSEM).} + +\item{count_type}{type to assign the values of \code{counts_dat} to in the \code{counts} slot} + +\item{sample_id_colname}{name of the column in \code{sample_metadata} that contains the sample IDs. (Default: \code{NULL} - +first column in the sample metadata will be used.)} + +\item{feature_id_colname}{name of the column in \code{counts_dat} that contains feature/gene IDs. (Default: \code{NULL} - first +column in the count data will be used.)} + +\item{delim}{Delimiter used in the input files. Any delimiter accepted by \code{readr::read_delim()} can be used. +If the files are in CSV format, set \code{delim = ','}; for TSV format, set \code{delim = '\\t'}.} + +\item{...}{additional arguments forwarded to \code{readr::read_delim()}.} +} +\value{ +\link{multiOmicDataSet} object +} +\description{ +Construct a multiOmicDataSet object from text files (e.g. TSV, CSV). +} +\examples{ +moo <- create_multiOmicDataSet_from_files( + sample_meta_filepath = system.file("extdata", + "sample_metadata.tsv.gz", + package = "MOSuite" + ), + feature_counts_filepath = system.file("extdata", + "RSEM.genes.expected_count.all_samples.txt.gz", + package = "MOSuite" + ), + delim = "\t" +) +moo@counts$raw |> head() +moo@sample_meta + +moo_nidap <- create_multiOmicDataSet_from_files( + system.file("extdata", "nidap", + "Sample_Metadata_Bulk_RNA-seq_Training_Dataset_CCBR.csv.gz", + package = "MOSuite" + ), + system.file("extdata", "nidap", "Raw_Counts.csv.gz", package = "MOSuite"), + delim = "," +) + +} +\seealso{ +Other moo constructors: +\code{\link[=create_multiOmicDataSet_from_dataframes]{create_multiOmicDataSet_from_dataframes()}}, +\code{\link[=multiOmicDataSet]{multiOmicDataSet()}} +} +\concept{moo constructors} diff --git a/code/MOSuite/man/diff_counts.Rd b/code/MOSuite/man/diff_counts.Rd new file mode 100644 index 0000000..bf72697 --- /dev/null +++ b/code/MOSuite/man/diff_counts.Rd @@ -0,0 +1,110 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/differential.R +\name{diff_counts} +\alias{diff_counts} +\title{Differential expression analysis} +\usage{ +diff_counts( + moo, + count_type = "filt", + sub_count_type = NULL, + sample_id_colname = NULL, + feature_id_colname = NULL, + samples_to_include = NULL, + covariates_colnames = NULL, + contrast_colname = NULL, + contrasts = NULL, + input_in_log_counts = FALSE, + return_mean_and_sd = FALSE, + voom_normalization_method = "quantile", + print_plots = options::opt("print_plots"), + save_plots = options::opt("save_plots"), + plots_subdir = "diff" +) +} +\arguments{ +\item{moo}{multiOmicDataSet object (see \code{create_multiOmicDataSet_from_dataframes()})} + +\item{count_type}{the type of counts to use -- must be a name in the counts slot (\code{moo@counts})} + +\item{sub_count_type}{if \code{count_type} is a list, specify the sub count type within the list. (Default: \code{NULL})} + +\item{sample_id_colname}{The column from the sample metadata containing the sample names. The names in this column +must exactly match the names used as the sample column names of your input Counts Matrix. (Default: \code{NULL} - first +column in the sample metadata will be used.)} + +\item{feature_id_colname}{The column from the counts data containing the Feature IDs (Usually Gene or Protein ID). +This is usually the first column of your input Counts Matrix. Only columns of Text type from your input Counts +Matrix will be available to select for this parameter. (Default: \code{NULL} - first column in the counts matrix will be +used.)} + +\item{samples_to_include}{Which samples would you like to include? Usually, you will choose all sample columns, or +you could choose to remove certain samples. Samples excluded here will be removed in this step and from further +analysis downstream of this step. (Default: \code{NULL} - all sample IDs in \code{moo@sample_meta} will be used.)} + +\item{covariates_colnames}{The column name(s) from the sample metadata containing variable(s) of interest, such as +phenotype. Most commonly this will be the same column selected for your Groups Column. Some experimental designs +may require that you add additional covariate columns here.} + +\item{contrast_colname}{The column in the metadata that contains the group variables you wish to find differential +expression between. Up to 2 columns (2-factor analysis) can be used.} + +\item{contrasts}{Specify each contrast in the format group1-group2, e.g. treated-control} + +\item{input_in_log_counts}{set this to \code{TRUE} if counts are already log2-transformed} + +\item{return_mean_and_sd}{if TRUE, return Mean and Standard Deviation of groups in addition to DEG estimates for +contrast(s)} + +\item{voom_normalization_method}{Normalization method to be applied to the logCPM values when using \code{limma::voom}} + +\item{print_plots}{Whether to print plots during analysis (Defaults to \code{FALSE}, overwritable using option 'moo_print_plots' or environment variable 'MOO_PRINT_PLOTS')} + +\item{save_plots}{Whether to save plots to files during analysis (Defaults to \code{TRUE}, overwritable using option 'moo_save_plots' or environment variable 'MOO_SAVE_PLOTS')} + +\item{plots_subdir}{subdirectory in \verb{figures/} where plots will be saved if \code{save_plots} is \code{TRUE}} +} +\value{ +\code{multiOmicDataSet} with \code{diff} added to the \code{analyses} slot (i.e. \code{moo@analyses$diff}) +} +\description{ +Differential expression analysis +} +\examples{ +moo <- multiOmicDataSet( + sample_metadata = as.data.frame(nidap_sample_metadata), + anno_dat = data.frame(), + counts_lst = list( + "raw" = as.data.frame(nidap_raw_counts), + "clean" = as.data.frame(nidap_clean_raw_counts), + "filt" = as.data.frame(nidap_filtered_counts) + ) +) |> + diff_counts( + count_type = "filt", + sub_count_type = NULL, + sample_id_colname = "Sample", + feature_id_colname = "Gene", + covariates_colnames = c("Group", "Batch"), + contrast_colname = c("Group"), + contrasts = c("B-A", "C-A", "B-C"), + voom_normalization_method = "quantile", + ) +head(moo@analyses$diff) +} +\seealso{ +Other moo methods: +\code{\link[=batch_correct_counts]{batch_correct_counts()}}, +\code{\link[=clean_raw_counts]{clean_raw_counts()}}, +\code{\link[=filter_counts]{filter_counts()}}, +\code{\link[=filter_diff]{filter_diff()}}, +\code{\link[=normalize_counts]{normalize_counts()}}, +\code{\link[=plot_corr_heatmap]{plot_corr_heatmap()}}, +\code{\link[=plot_expr_heatmap]{plot_expr_heatmap()}}, +\code{\link[=plot_histogram]{plot_histogram()}}, +\code{\link[=plot_pca]{plot_pca()}}, +\code{\link[=plot_read_depth]{plot_read_depth()}}, +\code{\link[=run_deseq2]{run_deseq2()}}, +\code{\link[=set_color_pal]{set_color_pal()}} +} +\concept{moo methods} diff --git a/code/MOSuite/man/do_math.Rd b/code/MOSuite/man/do_math.Rd new file mode 100644 index 0000000..79a56cf --- /dev/null +++ b/code/MOSuite/man/do_math.Rd @@ -0,0 +1,24 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/utils.R +\name{do_math} +\alias{do_math} +\title{Function for testing CLI argument parsing} +\usage{ +do_math(add = TRUE, subtract = FALSE, left = 1, right = 2) +} +\arguments{ +\item{add}{whether to add left and right} + +\item{subtract}{whether to subtract left and right} + +\item{left}{number on the left side of the operand} + +\item{right}{number on the right side of the operand} +} +\value{ +result of adding or subtracting left and right +} +\description{ +Function for testing CLI argument parsing +} +\keyword{internal} diff --git a/code/MOSuite/man/extract_counts.Rd b/code/MOSuite/man/extract_counts.Rd new file mode 100644 index 0000000..960be31 --- /dev/null +++ b/code/MOSuite/man/extract_counts.Rd @@ -0,0 +1,46 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/0_mo-class.R +\name{extract_counts} +\alias{extract_counts} +\alias{extract_counts,MOSuite::multiOmicDataSet-method} +\title{Extract count data} +\usage{ +extract_counts(moo, count_type, sub_count_type = NULL) + +## S7 method for class
}}\preformatted{options::opts(env = "MOSuite")
+
+options::opt(x, default, env = "MOSuite")
+}\if{html}{\out{
}}
+}
+
+\section{Options}{
+
+\describe{
+\item{print_plots}{\describe{
+Whether to print plots during analysis\item{default: }{\preformatted{FALSE}}
+\item{option: }{moo_print_plots}
+\item{envvar: }{MOO_PRINT_PLOTS (evaluated if possible, raw string otherwise)}
+}}
+
+\item{save_plots}{\describe{
+Whether to save plots to files during analysis\item{default: }{\preformatted{TRUE}}
+\item{option: }{moo_save_plots}
+\item{envvar: }{MOO_SAVE_PLOTS (evaluated if possible, raw string otherwise)}
+}}
+
+\item{plots_dir}{\describe{
+Path where plots are saved when \code{moo_save_plots} is \code{TRUE}\item{default: }{\preformatted{"figures/"}}
+\item{option: }{moo_plots_dir}
+\item{envvar: }{MOO_PLOTS_DIR (evaluated if possible, raw string otherwise)}
+}}
+
+}
+}
+
+\seealso{
+options getOption Sys.setenv Sys.getenv
+}
diff --git a/code/MOSuite/man/parse_optional_vector.Rd b/code/MOSuite/man/parse_optional_vector.Rd
new file mode 100644
index 0000000..291bee1
--- /dev/null
+++ b/code/MOSuite/man/parse_optional_vector.Rd
@@ -0,0 +1,26 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{parse_optional_vector}
+\alias{parse_optional_vector}
+\title{Parse comma-separated string into a vector}
+\usage{
+parse_optional_vector(x)
+}
+\arguments{
+\item{x}{character string with comma-separated values}
+}
+\value{
+character vector or NULL if input is empty
+}
+\description{
+Splits a comma-separated string into a trimmed character vector.
+Returns NULL if input is empty, NULL, or has zero length.
+}
+\examples{
+\dontrun{
+parse_optional_vector("a, b, c")
+parse_optional_vector("")
+}
+
+}
+\keyword{internal}
diff --git a/code/MOSuite/man/parse_samples_to_rename.Rd b/code/MOSuite/man/parse_samples_to_rename.Rd
new file mode 100644
index 0000000..6a9e7e9
--- /dev/null
+++ b/code/MOSuite/man/parse_samples_to_rename.Rd
@@ -0,0 +1,26 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{parse_samples_to_rename}
+\alias{parse_samples_to_rename}
+\title{Parse sample rename pairs from string}
+\usage{
+parse_samples_to_rename(x)
+}
+\arguments{
+\item{x}{character string with rename pairs in format "old:new,old2:new2"}
+}
+\value{
+named list with old names as keys and new names as values, or NULL if empty
+}
+\description{
+Parses a string containing sample rename pairs in format "old:new,old2:new2"
+and returns a named list where names are old sample names and values are new names.
+}
+\examples{
+\dontrun{
+parse_samples_to_rename("sample1:S1,sample2:S2")
+parse_samples_to_rename("")
+}
+
+}
+\keyword{internal}
diff --git a/code/MOSuite/man/parse_vector_with_default.Rd b/code/MOSuite/man/parse_vector_with_default.Rd
new file mode 100644
index 0000000..d4a5f01
--- /dev/null
+++ b/code/MOSuite/man/parse_vector_with_default.Rd
@@ -0,0 +1,28 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{parse_vector_with_default}
+\alias{parse_vector_with_default}
+\title{Parse comma-separated string with default fallback}
+\usage{
+parse_vector_with_default(x, default)
+}
+\arguments{
+\item{x}{character string with comma-separated values}
+
+\item{default}{default value to return if x is empty}
+}
+\value{
+character vector or default value
+}
+\description{
+Splits a comma-separated string into a trimmed character vector.
+Returns a default value if input is empty, NULL, or has zero length.
+}
+\examples{
+\dontrun{
+parse_vector_with_default("a, b, c", "default")
+parse_vector_with_default("", "default")
+}
+
+}
+\keyword{internal}
diff --git a/code/MOSuite/man/plot_corr_heatmap-data.frame.Rd b/code/MOSuite/man/plot_corr_heatmap-data.frame.Rd
new file mode 100644
index 0000000..0eec133
--- /dev/null
+++ b/code/MOSuite/man/plot_corr_heatmap-data.frame.Rd
@@ -0,0 +1,44 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plot_heatmap.R
+\name{plot_corr_heatmap,data.frame-method}
+\alias{plot_corr_heatmap,data.frame-method}
+\alias{plot_corr_heatmap.data.frame}
+\title{Plot correlation heatmap for counts dataframe}
+\arguments{
+\item{moo_counts}{a \code{data.frame} of counts}
+
+\item{sample_metadata}{sample metadata as a data frame or tibble (\strong{Required})}
+
+\item{sample_id_colname}{The column from the sample metadata containing the sample names. The names in this column
+must exactly match the names used as the sample column names of your input Counts Matrix. (Default: \code{NULL} - first
+column in the sample metadata will be used.)}
+
+\item{feature_id_colname}{The column from the counts data containing the Feature IDs (Usually Gene or Protein ID).
+This is usually the first column of your input Counts Matrix. Only columns of Text type from your input Counts
+Matrix will be available to select for this parameter. (Default: \code{NULL} - first column in the counts matrix will be
+used.)}
+
+\item{group_colname}{The column from the sample metadata containing the sample group information. This is usually a
+column showing to which experimental treatments each sample belongs (e.g. WildType, Knockout, Tumor, Normal,
+Before, After, etc.).}
+
+\item{label_colname}{The column from the sample metadata containing the sample labels as you wish them to appear in
+the plots produced by this template. This can be the same Sample Names Column. However, you may desire different
+labels to display on your figure (e.g. shorter labels are sometimes preferred on plots). In that case, select the
+column with your preferred Labels here. The selected column should contain unique names for each sample. (Default:
+\code{NULL} -- \code{sample_id_colname} will be used.)}
+
+\item{color_values}{vector of colors as hex values or names recognized by R}
+}
+\description{
+Plot correlation heatmap for counts dataframe
+}
+\seealso{
+\code{\link[=plot_corr_heatmap]{plot_corr_heatmap()}} generic
+
+Other plotters for counts dataframes:
+\code{\link{plot_histogram,data.frame-method}},
+\code{\link{plot_pca,data.frame-method}},
+\code{\link{plot_read_depth,data.frame-method}}
+}
+\concept{plotters for counts dataframes}
diff --git a/code/MOSuite/man/plot_corr_heatmap-multiOmicDataSet.Rd b/code/MOSuite/man/plot_corr_heatmap-multiOmicDataSet.Rd
new file mode 100644
index 0000000..0f09035
--- /dev/null
+++ b/code/MOSuite/man/plot_corr_heatmap-multiOmicDataSet.Rd
@@ -0,0 +1,28 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plot_heatmap.R
+\name{plot_corr_heatmap,MOSuite::multiOmicDataSet-method}
+\alias{plot_corr_heatmap,MOSuite::multiOmicDataSet-method}
+\alias{plot_corr_heatmap.multiOmicDataSet}
+\title{Plot correlation heatmap for multiOmicDataSet}
+\arguments{
+\item{moo_counts}{a \code{multiOmicDataSet} object}
+
+\item{count_type}{the type of counts to use. Must be a name in the counts slot (\code{names(moo@counts)}).}
+
+\item{sub_count_type}{used if \code{count_type} is a list in the counts slot: specify the sub count type within the list.
+Must be a name in \code{names(moo@counts[[count_type]])}.}
+
+\item{...}{additional arguments forwarded to \code{\link[=plot_corr_heatmap]{plot_corr_heatmap()}} for \code{data.frame}}
+}
+\description{
+Plot correlation heatmap for multiOmicDataSet
+}
+\seealso{
+\code{\link[=plot_corr_heatmap]{plot_corr_heatmap()}} generic
+
+Other plotters for multiOmicDataSets:
+\code{\link{plot_histogram,MOSuite::multiOmicDataSet-method}},
+\code{\link{plot_pca,MOSuite::multiOmicDataSet-method}},
+\code{\link{plot_read_depth,MOSuite::multiOmicDataSet-method}}
+}
+\concept{plotters for multiOmicDataSets}
diff --git a/code/MOSuite/man/plot_corr_heatmap.Rd b/code/MOSuite/man/plot_corr_heatmap.Rd
new file mode 100644
index 0000000..f09d191
--- /dev/null
+++ b/code/MOSuite/man/plot_corr_heatmap.Rd
@@ -0,0 +1,96 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plot_heatmap.R
+\name{plot_corr_heatmap}
+\alias{plot_corr_heatmap}
+\title{Plot correlation heatmap}
+\usage{
+plot_corr_heatmap(moo_counts, ...)
+}
+\arguments{
+\item{moo_counts}{counts dataframe or \code{multiOmicDataSet} containing \code{count_type} & \code{sub_count_type} in the counts
+slot}
+
+\item{...}{arguments forwarded to method}
+}
+\value{
+heatmap from \code{ComplexHeatmap::Heatmap()}
+}
+\description{
+Plot correlation heatmap
+}
+\details{
+\subsection{Method Usage}{
+
+\if{html}{\out{}}\preformatted{# multiOmicDataSet
+plot_corr_heatmap(moo_counts,
+ count_type,
+ sub_count_type = NULL,
+ ...)
+
+# dataframe
+plot_corr_heatmap(moo_counts,
+ sample_metadata,
+ sample_id_colname = NULL,
+ feature_id_colname = NULL,
+ group_colname = "Group",
+ label_colname = "Label",
+ color_values = c(
+ "#5954d6", "#e1562c", "#b80058", "#00c6f8", "#d163e6", "#00a76c",
+ "#ff9287", "#008cf9", "#006e00", "#796880", "#FFA500", "#878500"
+ ))
+}\if{html}{\out{
}}
+}
+}
+\examples{
+# plot correlation heatmap for a counts slot in a multiOmicDataset Object
+moo <- multiOmicDataSet(
+ sample_metadata = as.data.frame(nidap_sample_metadata),
+ anno_dat = data.frame(),
+ counts_lst = list("raw" = as.data.frame(nidap_raw_counts))
+)
+p <- plot_corr_heatmap(moo, count_type = "raw")
+
+# plot correlation heatmap for a counts dataframe
+plot_corr_heatmap(
+ moo@counts$raw,
+ sample_metadata = moo@sample_meta,
+ sample_id_colname = "Sample",
+ feature_id_colname = "Gene",
+ group_colname = "Group",
+ label_colname = "Label"
+)
+}
+\seealso{
+\itemize{
+\item \code{\link[=plot_corr_heatmap.multiOmicDataSet]{plot_corr_heatmap.multiOmicDataSet()}}
+\item \code{\link[=plot_corr_heatmap.data.frame]{plot_corr_heatmap.data.frame()}}
+}
+
+Other plotters:
+\code{\link[=plot_expr_heatmap]{plot_expr_heatmap()}},
+\code{\link[=plot_histogram]{plot_histogram()}},
+\code{\link[=plot_pca]{plot_pca()}},
+\code{\link[=plot_read_depth]{plot_read_depth()}},
+\code{\link[=print_or_save_plot]{print_or_save_plot()}}
+
+Other heatmaps:
+\code{\link[=plot_expr_heatmap]{plot_expr_heatmap()}}
+
+Other moo methods:
+\code{\link[=batch_correct_counts]{batch_correct_counts()}},
+\code{\link[=clean_raw_counts]{clean_raw_counts()}},
+\code{\link[=diff_counts]{diff_counts()}},
+\code{\link[=filter_counts]{filter_counts()}},
+\code{\link[=filter_diff]{filter_diff()}},
+\code{\link[=normalize_counts]{normalize_counts()}},
+\code{\link[=plot_expr_heatmap]{plot_expr_heatmap()}},
+\code{\link[=plot_histogram]{plot_histogram()}},
+\code{\link[=plot_pca]{plot_pca()}},
+\code{\link[=plot_read_depth]{plot_read_depth()}},
+\code{\link[=run_deseq2]{run_deseq2()}},
+\code{\link[=set_color_pal]{set_color_pal()}}
+}
+\concept{heatmaps}
+\concept{moo methods}
+\concept{plotters}
+\keyword{plotters}
diff --git a/code/MOSuite/man/plot_expr_heatmap.Rd b/code/MOSuite/man/plot_expr_heatmap.Rd
new file mode 100644
index 0000000..8f8b890
--- /dev/null
+++ b/code/MOSuite/man/plot_expr_heatmap.Rd
@@ -0,0 +1,376 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plot_heatmap.R
+\name{plot_expr_heatmap}
+\alias{plot_expr_heatmap}
+\alias{plot_expr_heatmap,MOSuite::multiOmicDataSet-method}
+\alias{plot_expr_heatmap,data.frame-method}
+\title{Plot expression heatmap}
+\usage{
+plot_expr_heatmap(
+ moo_counts,
+ count_type,
+ sub_count_type = NULL,
+ sample_metadata = NULL,
+ sample_id_colname = NULL,
+ feature_id_colname = NULL,
+ group_colname = "Group",
+ label_colname = NULL,
+ samples_to_include = NULL,
+ color_values = c("#5954d6", "#e1562c", "#b80058", "#00c6f8", "#d163e6", "#00a76c",
+ "#ff9287", "#008cf9", "#006e00", "#796880", "#FFA500", "#878500"),
+ include_all_genes = FALSE,
+ filter_top_genes_by_variance = TRUE,
+ top_genes_by_variance_to_include = 500,
+ specific_genes_to_include_in_heatmap = "None",
+ cluster_genes = TRUE,
+ gene_distance_metric = "correlation",
+ gene_clustering_method = "average",
+ display_gene_dendrograms = TRUE,
+ display_gene_names = FALSE,
+ center_and_rescale_expression = TRUE,
+ cluster_samples = FALSE,
+ arrange_sample_columns = TRUE,
+ order_by_gene_expression = FALSE,
+ gene_to_order_columns = " ",
+ gene_expression_order = "low_to_high",
+ smpl_distance_metric = "correlation",
+ smpl_clustering_method = "average",
+ display_smpl_dendrograms = TRUE,
+ reorder_dendrogram = FALSE,
+ reorder_dendrogram_order = c(),
+ display_sample_names = TRUE,
+ group_columns = c("Group", "Replicate", "Batch"),
+ assign_group_colors = FALSE,
+ assign_color_to_sample_groups = c(),
+ group_colors = c("#5954d6", "#e1562c", "#b80058", "#00c6f8", "#d163e6", "#00a76c",
+ "#ff9287", "#008cf9", "#006e00", "#796880", "#FFA500", "#878500"),
+ heatmap_color_scheme = "Default",
+ autoscale_heatmap_color = TRUE,
+ set_min_heatmap_color = -2,
+ set_max_heatmap_color = 2,
+ aspect_ratio = "Auto",
+ legend_font_size = 10,
+ gene_name_font_size = 4,
+ sample_name_font_size = 8,
+ display_numbers = FALSE,
+ plot_filename = "expr_heatmap.png",
+ print_plots = options::opt("print_plots"),
+ save_plots = options::opt("save_plots"),
+ plots_subdir = "heatmap"
+)
+
+## S7 method for class