Get Rid of "MainFactor" inDEseq2 analysis

ICB-DCM · Nov 6, 2024 · b7dfce8 · b7dfce8
1 parent dd54131
commit b7dfce8
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Showing 3 changed files with 16 additions and 44 deletions.
diff --git a/program/shinyApp/R/pre_processing/ui.R b/program/shinyApp/R/pre_processing/ui.R
@@ -20,7 +20,6 @@ pre_processing_sidebar_panel <- sidebarPanel(
     ),
     selected = "none"
   ) %>% helper(type = "markdown", content = "PreProcessing_Procedures"),
-  uiOutput(outputId = "DESeq_formula_main_ui"),
   uiOutput(outputId = "DESeq_formula_sub_ui"),
   uiOutput(outputId = "batch_effect_ui"),
   actionButton(

diff --git a/program/shinyApp/R/pre_processing/util.R b/program/shinyApp/R/pre_processing/util.R
@@ -94,39 +94,26 @@ ln_normalisation <- function(data, omic_type, logarithm_procedure){
 
 
 deseq_processing <- function(
-  data, omic_type, formula_main, formula_sub, session_token, batch_correct
+  data, omic_type, formula_sub, session_token, batch_correct
 ){
   # Center and scale the data
   # prefilter the data
   data <- prefiltering(data, omic_type)
   # DESeq2
   if(omic_type == "Transcriptomics"){
-    design_formula <- paste("~", formula_main)
-    # only do this locally
-    colData(data)[,formula_main] <- as.factor(
-      colData(data)[,formula_main]
-    )
-    if(length(formula_sub) > 0){
-      design_formula <- paste(
-        design_formula, " + ",
-        paste(formula_sub, collapse = " + ")
-      )
-      # turn each factor into a factor
-      for(i in formula_sub){
-        colData(data)[,i] <- as.factor(
-          colData(data)[,i]
-        )
-      }
-      par_tmp[[session_token]][["DESeq_factors"]] <<- c(
-        formula_main,formula_sub
+    if(length(formula_sub) <= 0){
+      stop(
+        "Please select at least one factor for the DESeq2 analysis.",
+        class = "InvalidInputError"
       )
     }
-    else{
-      par_tmp[[session_token]][["DESeq_factors"]] <<- c(formula_main)
+    design_formula <- paste("~", paste(formula_sub, collapse = " + "))
+    # turn each factor into a factor
+    for(i in formula_sub){
+      colData(data)[,i] <- as.factor(colData(data)[,i])
     }
+    par_tmp[[session_token]][["DESeq_factors"]] <<- c(formula_sub)
     print(design_formula)
-    # on purpose local
-    print(colData(data)[,formula_main])
 
     dds <- DESeq2::DESeqDataSetFromMatrix(
       countData = assay(data),

diff --git a/program/shinyApp/server.R b/program/shinyApp/server.R
@@ -871,7 +871,7 @@ server <- function(input,output,session){
       length(unique(colData(res_tmp[[session$token]]$data_original)[[col]])) < nrow(colData(res_tmp[[session$token]]$data_original))
     })]
     if (input$PreProcessing_Procedure == "vst_DESeq") {
-      filtered_column_names <- filtered_column_names[!filtered_column_names %in% c(input$DESeq_formula_main, input$DESeq_formula_sub)]
+      filtered_column_names <- filtered_column_names[!filtered_column_names %in% c(input$DESeq_formula_sub)]
     }
     selectInput(
       inputId = "BatchEffect_Column",
@@ -880,28 +880,14 @@ server <- function(input,output,session){
       selected = "NULL"
     )
   })
-  output$DESeq_formula_main_ui <- renderUI({
-    req(data_input_shiny())
-    req(input$PreProcessing_Procedure == "vst_DESeq")
-    selectInput(
-      inputId = "DESeq_formula_main",
-      label = paste0(
-        "Choose main factor for desing formula in DESeq pipeline ",
-        "(App might crash if your factor as only 1 sample per level)"
-      ),
-      choices = c(colnames(colData(res_tmp[[session$token]]$data))),
-      multiple = F,
-      selected = "condition"
-    ) %>% helper(type = "markdown", content = "PreProcessing_DESeqMain")
-  })
   output$DESeq_formula_sub_ui <- renderUI({
     req(data_input_shiny())
     req(input$PreProcessing_Procedure == "vst_DESeq")
     selectInput(
       inputId = "DESeq_formula_sub",
       label = paste0(
-        "Choose other factors to account for",
-        "(App might crash if your factor as only 1 sample per level)"
+        "Choose factors to account for ",
+        "(App might crash if your factor has only 1 sample per level)"
       ),
       choices = c(colnames(colData(res_tmp[[session$token]]$data))),
       multiple = T,
@@ -943,7 +929,6 @@ server <- function(input,output,session){
         res_tmp[[session$token]]$data <<- deseq_processing(
             data = res_tmp[[session$token]]$data,
             omic_type = par_tmp[[session$token]]$omic_type,
-            formula_main = input$DESeq_formula_main,
             formula_sub = input$DESeq_formula_sub,
             session_token = session$token,
             batch_correct = F
@@ -979,7 +964,6 @@ server <- function(input,output,session){
         res_tmp[[session$token]]$data_batch_corrected <<- deseq_processing(
           data = tmp_data_selected,
           omic_type = par_tmp[[session$token]]$omic_type,
-          formula_main = input$DESeq_formula_main,
           formula_sub = c(input$DESeq_formula_sub, input$BatchEffect_Column),
           session_token = session$token,
           batch_correct = T
@@ -1083,7 +1067,9 @@ server <- function(input,output,session){
       message = paste0(
         "**PreProcessing** - Preprocessing procedure -specific (user-chosen): ",
         ifelse(input$PreProcessing_Procedure == "vst_DESeq",
-               paste0(input$PreProcessing_Procedure, "~",input$DESeq_formula_main),
+               paste0(
+                 input$PreProcessing_Procedure,
+                 " ~ ",paste(input$DESeq_formula_sub, collapse=" + ")),
                input$PreProcessing_Procedure)
       )
     )