Merging updated function of GSEA

DESCRIPTION

@@ -29,10 +29,10 @@ Imports:
     scales,
     grid,
     utils,
-    patchwork
+    patchwork,
+    cowplot
 Suggests: 
     biomaRt,
-    cowplot,
     dbscan,
     ggnewscale,
     ggrepel,

NAMESPACE

@@ -1,24 +1,25 @@
 # Generated by roxygen2: do not edit by hand
 
 export(add_annotations)
-export(barplot_GSEA)
 export(detect_filter)
 export(get_annotations)
 export(get_stars)
-export(heatmap_GSEA)
-export(merge_GSEA)
+export(heatmap_PA)
+export(merge_PA)
 export(nice_KM)
 export(nice_PCA)
 export(nice_UMAP)
 export(nice_VSB)
 export(nice_Volcano)
 export(nice_tSNE)
-export(plot_GSEA)
+export(plot_PA)
 export(power_analysis)
 export(save_results)
 export(split_cases)
 export(tpm)
 import(ggplot2)
+importFrom(cowplot,get_legend)
 importFrom(magrittr,"%>%")
 importFrom(patchwork,plot_layout)
 importFrom(rlang,.data)
+importFrom(utils,modifyList)

R/heatmap_GSEA.R → R/heatmap_PA.R

@@ -1,10 +1,10 @@
 #########################
-# Function heatmap_GSEA #
+# Function heatmap_PA #
 #########################
 
-#' Plot leading edge heatmaps from GSEA results.
+#' Plot leading edge heatmaps from GSEA/CAMERA/PADOG results.
 #'
-#' Generates heatmaps of leading edge genes for each gene set from GSEA output.
+#' Generates heatmaps based on normalized data of genes for each gene set from GSEA/CAMERA/PADOG output.
 #'
 #' @param main_dir Optional base directory. If supplied, it will be prepended to all relative file paths.
 #' @param expression_file Path to the expression data file (tab-delimited) or relative to main_dir.
@@ -19,10 +19,15 @@
 #' @return Saves one PDF and one JPG heatmap per gene set under output_dir; optionally saves intermediate TSV.
 #' @export
 
-heatmap_GSEA <- function(main_dir = NULL, expression_file, metadata_file, gmt_file,
+heatmap_PA <- function(main_dir = NULL, expression_file, metadata_file, gmt_file,
                          ranked_genes_file, gsea_file, output_dir = "leading_edge_heatmaps",
                          sample_col = "Sample", group_col = "group", save_dataframe = FALSE)
 {
+  # Avoid check NOTES for global variables across multiple functions
+  utils::globalVariables(c(
+    "NAME", "GENES", "SIZE", "tags", "L.EDGE_size"
+  ))
+
   # Ensure required packages are installed
   if (!requireNamespace("readr", quietly = TRUE)) stop("Package \"readr\" must be installed to use this function.", call. = FALSE)
   if (!requireNamespace("grDevices", quietly = TRUE)) stop("Package \"grDevices\" must be installed to use this function.", call. = FALSE)

R/merge_GSEA.R → R/merge_PA.R

@@ -1,19 +1,24 @@
 #######################
-# Function merge_GSEA #
+# Function merge_PA #
 #######################
 
 #' Merge GSEA results data frames.
 #'
-#' After running GSEA_all.sh from GSEA.sh, merge_GSEA function joins .tsv files to a single file
+#' After running GSEA_all.sh from GSEA.sh, merge_PA function joins .tsv files to a single file
 #'
 #' @param input_directory The directory containing the GSEA collection results in TSV format.
 #' @param output_file The output file to save the merged data. If not provided, the file will be saved in the input directory.
 #' @importFrom magrittr %>%
 #' @export
-
-
-merge_GSEA <- function(input_directory, output_file = "collections_merged_gsea_data.tsv") {
-
+merge_PA <- function(input_directory, output_file = "collections_merged_gsea_data.tsv") {
+
+  # Avoid check NOTES for global variables across multiple functions
+  utils::globalVariables(c(
+    "...12", "numeric_cols", "LEADING EDGE", "tags", "signal",
+    "FDR q-val", "Log10FDR", "FWER p-val", "Comparison"
+  ))
+
+  # Ensure required packages are installed
   if (!requireNamespace("dplyr", quietly = TRUE)) stop("Package \"dplyr\" must be installed to use this function.", call. = FALSE)
   if (!requireNamespace("readr", quietly = TRUE)) stop("Package \"readr\" must be installed to use this function.", call. = FALSE)
   if (!requireNamespace("tidyr", quietly = TRUE)) stop("Package \"tidyr\" must be installed to use this function.", call. = FALSE)