PCA scaling

program/shinyApp/R/C.R

@@ -34,15 +34,15 @@ MANUALLY <- FALSE # change to TRUE, if you want to set the paths manually
 
 if(MANUALLY){
   # Adjust the path to the data file
-  envList <- readRDS('path/to/Data.rds')
+  envList <- readRDS('path/to/Data.RDS')
   # Adjust the path to the utils.R file
   source('path/to/utils.R')
   print('Path manually set')
 }else{
   # if you get an error try to set paths manually
   # remember to set MANUALLY <- TRUE
   direcoty_of_files <- dirname(rstudioapi::getSourceEditorContext()$path)
-  envList <- readRDS(paste0(direcoty_of_files,'/','Data.rds'))
+  envList <- readRDS(paste0(direcoty_of_files,'/','Data.RDS'))
   if('utils.R' %in% list.files(direcoty_of_files)){
     source(file.path(direcoty_of_files,'utils.R'))
   }

program/shinyApp/R/fun_getCodeSnippets.R

@@ -235,7 +235,7 @@ lapply(ls(pattern="violin"), get)
 pca <- prcomp(
   x = as.data.frame(t(assay(res_tmp$data))),
   center = T,
-  scale. = FALSE
+  scale. = ifelse(par_tmp$PCA$scale_data == "Yes",T,F)
 )
 
 pcaData <- data.frame(pca$x,colData(res_tmp$data))

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

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"),