OA now correctly takes preprocessing argument into account (#159)

* OA now correctly takes into account whether you want the gene list before or after preprocessing. * Update program/shinyApp/R/pca/server.R Co-authored-by: Lea Seep <[email protected]> --------- Co-authored-by: Lea Seep <[email protected]>
ICB-DCM · Jan 24, 2024 · 5c06cce · 5c06cce
1 parent c864c9f
commit 5c06cce
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Showing 2 changed files with 14 additions and 12 deletions.
diff --git a/program/shinyApp/R/enrichment_analysis/overrepresentation_analysis.R b/program/shinyApp/R/enrichment_analysis/overrepresentation_analysis.R
@@ -11,23 +11,25 @@ over_representation_analysis <- function(
 
   if(!isTruthy(input$UniverseOfGene)){
     universeSelected_tranlsated <- NULL
-  }else{
-    if(input$UniverseOfGene == "default"){
-      universeSelected_tranlsated <- NULL
-    }
-  }
-  # TODO: workaround and is needed?
-  if(input$UniverseOfGene == "allPresentGenes_before_pre_process"){
+  } else if(input$UniverseOfGene == "default"){
+    universeSelected_tranlsated <- NULL
+  } else {
+    # TODO: only works with ENSEMBL IDs at the moment
     req(data_input_shiny())
-    universeSelected <- rownames(data)
+    if(input$UniverseOfGene == "after_pre_process"){
+      universeSelected <- rownames(data$data)
+    } else if(input$UniverseOfGene == "before_pre_process"){
+      universeSelected <- rownames(data$data_original)
+    }
     # Note if transcripts are used this will be ignored for enrichment analysis
     universeSelected <- unique(gsub("\\..*$","",universeSelected))
     print(paste0("Universe genes untranslated: ",length(universeSelected)))
     universeSelected_tranlsated <- bitr(
       universeSelected,
       fromType = "ENSEMBL",
       toType = "ENTREZID",
-      OrgDb = ifelse(input$OrganismChoice == "hsa","org.Hs.eg.db","org.Mm.eg.db"))$ENTREZID
+      OrgDb = ifelse(input$OrganismChoice == "hsa","org.Hs.eg.db","org.Mm.eg.db")
+    )$ENTREZID
     print(paste0(
       "Universe genes translated (hence actually used): ",
       length(universeSelected_tranlsated)

diff --git a/program/shinyApp/R/enrichment_analysis/server.R b/program/shinyApp/R/enrichment_analysis/server.R
@@ -546,8 +546,8 @@ enrichment_analysis_Server <- function(id, data, params, updates){
               label = "Select an Universe for enrichment (default is clusterProfilers default",
               choices = c(
                 "default",
-                "allPresentGenes_after_pre_process",
-                "allPresentGenes_before_pre_process"
+                "after_pre_process",
+                "before_pre_process"
               ),
               selected = "default"
             )
@@ -797,7 +797,7 @@ enrichment_analysis_Server <- function(id, data, params, updates){
               input,
               output,
               ea_reactives$tmp_genes,
-              ea_reactives$data,
+              data,
               ea_reactives$enrichments2do,
               input$test_correction
             )