genesymbols in reports corrected

seoanezonjic · Oct 22, 2024 · 7a49817 · 7a49817
1 parent d8a4e3f
commit 7a49817
Show file tree

Hide file tree

Showing 2 changed files with 10 additions and 4 deletions.
diff --git a/R/main_clusters_to_enrichment.R b/R/main_clusters_to_enrichment.R
@@ -30,7 +30,8 @@ main_clusters_to_enrichment <- function(
   qvalcutoff = 0.2,
   all_custom_gmt = NULL,
   kegg_data_file = NULL,
-  universe = NULL){
+  universe = NULL, 
+  readable = TRUE){
 
   gene_attributes <- NULL
   gene_attribute_name <- NULL
@@ -51,6 +52,7 @@ main_clusters_to_enrichment <- function(
     }
     names(cluster_genes_list) <- cluster_genes[,1]
 
+
     enrichments_ORA <- multienricher_ora(all_funsys =  all_funsys, 
                                   genes_list =  cluster_genes_list, 
                                   task_size = task_size, 
@@ -61,7 +63,7 @@ main_clusters_to_enrichment <- function(
                                   custom_sets = all_custom_gmt,
                                   kegg_file = kegg_data_file,
                                   universe = universe,
-                                  readable = FALSE)
+                                  readable = readable)
 
 
     save(enrichments_ORA, file = temp_file)

diff --git a/inst/scripts/clusters_to_enrichment.R b/inst/scripts/clusters_to_enrichment.R
@@ -99,7 +99,8 @@ current_organism_info <- organisms_table[rownames(organisms_table) %in% opt$mode
 org_db <- get_org_db(current_organism_info)
 
 #Load universe
-if (is.null(opt$universe) || length(opt$universe) == 0){
+readable <-TRUE
+ if (is.null(opt$universe) || length(opt$universe) == 0){
   universe <- opt$universe
 }else if (file.exists(opt$universe)){
   universe <- read.table(opt$universe)[,1]
@@ -109,6 +110,8 @@ if (is.null(opt$universe) || length(opt$universe) == 0){
                                     output_id="ENTREZID",
                                     org_db = org_db, 
                                     just_output_ids=TRUE)
+  } else {
+    readable <- FALSE
   }
 }
 
@@ -149,7 +152,8 @@ ce_list <- main_clusters_to_enrichment(
   qvalcutoff = opt$qvalcutoff,
   all_custom_gmt = all_custom_gmt,
   kegg_data_file = kegg_data_file,
-  universe = universe
+  universe = universe,
+  readable = readable
 )
 enrichments_ORA <- ce_list[["enrichments_ORA"]]