Add option whether to scale data to unit variance

ICB-DCM · Oct 23, 2024 · 59e232e · 59e232e
1 parent 109750a
commit 59e232e
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Showing 2 changed files with 14 additions and 3 deletions.
diff --git a/program/shinyApp/R/pca/server.R b/program/shinyApp/R/pca/server.R
@@ -130,7 +130,8 @@ pca_Server <- function(id, data, params, row_select){
         check <- check_calculations(list(
           sample_selection_pca = input$sample_selection_pca,
           SampleAnnotationTypes_pca = input$SampleAnnotationTypes_pca,
-          batch = ifelse(par_tmp[[session$token]]$BatchColumn != "NULL" && input$UseBatch == "Yes",T,F)
+          batch = ifelse(par_tmp[[session$token]]$BatchColumn != "NULL" && input$UseBatch == "Yes",T,F),
+          scale_data = input$scale_data
         ), "PCA")
         if (check == "No Result yet"){
           output$PCA_Info <- renderText("PCA computed.")
@@ -200,7 +201,7 @@ pca_Server <- function(id, data, params, row_select){
             pca <- prcomp(
               x = as.data.frame(t(as.data.frame(assay(data2plot)))),
               center = T,
-              scale. = FALSE
+              scale. = ifelse(input$scale_data == "Yes",T,F)
             )
           }, error = function(e){
             error_modal(e)
@@ -223,7 +224,9 @@ pca_Server <- function(id, data, params, row_select){
           # assign par_temp as empty list
           par_tmp[[session$token]][["PCA"]] <<- list(
             sample_selection_pca = input$sample_selection_pca,
-            SampleAnnotationTypes_pca = input$SampleAnnotationTypes_pca
+            SampleAnnotationTypes_pca = input$SampleAnnotationTypes_pca,
+            batch = ifelse(par_tmp[[session$token]]$BatchColumn != "NULL" && input$UseBatch == "Yes",T,F),
+            scale_data = input$scale_data
           )
         } else {
           # otherwise read the reactive values

diff --git a/program/shinyApp/R/pca/ui.R b/program/shinyApp/R/pca/ui.R
@@ -16,6 +16,14 @@ pca_sidebar_panel <- function(ns){
     ),
     uiOutput(outputId = ns("SampleAnnotationTypes_pca_ui")),
     uiOutput(outputId = ns("sample_selection_pca_ui")),
+    # Scale data to unit variance y/n
+    radioGroupButtons(
+      inputId = ns("scale_data"),
+      label = "Scale data to unit variance?",
+      choices = c("Yes","No"),
+      direction = "horizontal",
+      selected = "No"
+    ),
     ### start pca ---
     actionButton(
       inputId = ns("Do_PCA"),