From bb5cbd0089c187a6cd3970af103c7b74beb59af4 Mon Sep 17 00:00:00 2001
From: PaulJonasJost <jost.pauljonas@gmail.com>
Date: Tue, 30 Jan 2024 13:11:44 +0100
Subject: [PATCH] Mainly spacing and replacing = with =

---
 .../shinyApp/R/heatmap/fun_entitieSelection.R | 74 +++++++++----------
 1 file changed, 33 insertions(+), 41 deletions(-)

diff --git a/program/shinyApp/R/heatmap/fun_entitieSelection.R b/program/shinyApp/R/heatmap/fun_entitieSelection.R
index 25b4dac4..cb835c37 100644
--- a/program/shinyApp/R/heatmap/fun_entitieSelection.R
+++ b/program/shinyApp/R/heatmap/fun_entitieSelection.R
@@ -1,56 +1,52 @@
-entitieSelection=function(data,
-                          type,
-                          TopK2Show=NA,
-                          additionalInput_row_anno=NA,
-                          additionalInput_row_anno_factor=NA,
-                          additionalInput_sample_annotation_types=NA,
-                          additionalInput_ctrl_idx=NA,
-                          additionalInput_cmp_idx=NA,
-                          psig_threhsold=NA){
+entitieSelection <- function(
+  data,
+  type,
+  TopK2Show=NA,
+  additionalInput_row_anno=NA,
+  additionalInput_row_anno_factor=NA,
+  additionalInput_sample_annotation_types=NA,
+  additionalInput_ctrl_idx=NA,
+  additionalInput_cmp_idx=NA,
+  psig_threhsold=NA
+){
   # to cover: c("TopK","significant_LFC","LFC_onlySig","rowAnno_based")
-  filtered_data=assay(data)
-  orderMakesSense_flag=FALSE
+  filtered_data <- assay(data)
+  orderMakesSense_flag <- FALSE
   print("Entitie Selection")
-  #print(additionalInput_row_anno)
   if(any(type=="rowAnno_based") & !(any(is.na(additionalInput_row_anno) &is.na(additionalInput_row_anno_factor))) & !any(additionalInput_row_anno_factor=="all")){
     # Note here this only what to show, LFCs and more importantly multiple test correction will be done on the entire set (without the row anno based selection!!)
     if(any(additionalInput_row_anno_factor=="all")){
-      filtered_data = filtered_data
-    }else{
-      filtered_data = filtered_data[which(data$annotation_rows[,additionalInput_row_anno] %in% additionalInput_row_anno_factor),]
+      filtered_data <- filtered_data
+    } else{
+      filtered_data <- filtered_data[which(data$annotation_rows[, additionalInput_row_anno] %in% additionalInput_row_anno_factor),]
     }
   }
   if(!(is.na(additionalInput_sample_annotation_types)) & !(is.na(additionalInput_ctrl_idx)) & !(is.na(additionalInput_cmp_idx))){
     if(any(type=="significant_LFC")){
-      # sort based on significance
-      # need LFCs
-      # is reachable from here? selectedData_processed()[[input$omicType]]$sample_table
+      # sort based on significance need LFCs
       ctrl_samples_idx <- which(colData(data)[,additionalInput_sample_annotation_types]%in%additionalInput_ctrl_idx)
       comparison_samples_idx <- which(colData(data)[,additionalInput_sample_annotation_types]%in%additionalInput_cmp_idx)
       if((length(ctrl_samples_idx) <= 1) | (length(comparison_samples_idx) <= 1)){
         warning("LFC makes no sense just having a single sample per conidition, which is here the case!")
-        filtered_data=NULL
-      }else{
-        LFC_output=getLFC(filtered_data,ctrl_samples_idx,comparison_samples_idx)
-        filtered_data=filtered_data[rownames(LFC_output)[order(LFC_output$p_adj,decreasing = F)],,drop=F]
-        orderMakesSense_flag=T
+        filtered_data <- NULL
+      } else{
+        LFC_output <- getLFC(filtered_data, ctrl_samples_idx, comparison_samples_idx)
+        filtered_data <- filtered_data[rownames(LFC_output)[order(LFC_output$p_adj, decreasing = F)],, drop=F]
+        orderMakesSense_flag <- T
       }
-      
     }
     if(any(type=="LFC_onlySig")){
       ctrl_samples_idx<-which(colData(data)[,additionalInput_sample_annotation_types]%in%additionalInput_ctrl_idx)
       comparison_samples_idx<-which(colData(data)[,additionalInput_sample_annotation_types]%in%additionalInput_cmp_idx)
-      LFC_output=getLFC(filtered_data,ctrl_samples_idx,comparison_samples_idx)
+      LFC_output <- getLFC(filtered_data, ctrl_samples_idx, comparison_samples_idx)
       if(!(any(LFC_output$p_adj<psig_threhsold))){
         warning("No single entry left! Maybe adjust psig_threhsold_heatmap (but do not put it arbitraly high!)")
-        #req(FALSE) -> can we speak from here to output$debug?
-        filtered_data=NULL
-      }else{
-        filtered_data=filtered_data[rownames(LFC_output)[which(LFC_output$p_adj<psig_threhsold)],,drop=F]
-        filtered_data=filtered_data[rownames(LFC_output)[order(LFC_output$LFC,decreasing = F)],,drop=F]
-        orderMakesSense_flag=T
+        filtered_data <- NULL
+      } else{
+        filtered_data <- filtered_data[rownames(LFC_output)[which(LFC_output$p_adj<psig_threhsold)],, drop=F]
+        filtered_data <- filtered_data[rownames(LFC_output)[order(LFC_output$LFC, decreasing = F)],, drop=F]
+        orderMakesSense_flag <- T
       }
-      
     }
   }
   
@@ -58,17 +54,13 @@ entitieSelection=function(data,
     if(orderMakesSense_flag){
       #assumes the data to be sorted somehow
       if(nrow(filtered_data)>TopK2Show){
-        filtered_data=filtered_data[c(1:TopK2Show),,drop=F]
-      }else{
-        filtered_data=filtered_data
+        filtered_data <- filtered_data[c(1:TopK2Show),, drop=F]
+      } else{
+        filtered_data <- filtered_data
       }
-    }else{
-      filtered_data=NULL
+    } else{
+      filtered_data <- NULL
     }
-    
   }
-  
-  
-  
   return(filtered_data)
 }