[FEAT] - scale and center option added to the PCA box

R/interface_module_box_readscp.R

@@ -54,6 +54,11 @@ box_readscp_ui <- function(id) {
                     label = "Convert zeros to NA",
                     value = TRUE
                 ),
+                checkboxInput(
+                    inputId = NS(id, "singlecell"),
+                    label = "Single cell data",
+                    value = FALSE
+                ),
                 actionButton(
                     inputId = NS(id, "convert"),
                     "Convert to a QFeatures object"

R/interface_module_qc_metrics.R

@@ -91,6 +91,16 @@ interface_module_pca_box <- function(id, title) {
                 label = "Color by",
                 choices = NULL
             ),
+            checkboxInput(
+                inputId = NS(id, "scale"),
+                label = "Scale data",
+                value = TRUE
+            ),
+            checkboxInput(
+                inputId = NS(id, "center"),
+                label = "Center data",
+                value = TRUE
+            ),
             checkboxInput(
                 inputId = NS(id, "show_legend"),
                 label = "Show Legend",

R/server_module_qc_metrics.R

@@ -62,7 +62,7 @@ server_module_qc_metrics <- function(id, assays_to_process, type) {
 #' @importFrom pcaMethods pca scores
 #' @importFrom methods is
 #'
-server_module_pca_box <- function(id, single_assay, method, transpose) {
+server_module_pca_box <- function(id, single_assay,  method, transpose) {
     moduleServer(id, function(input, output, session) {
         annotation_names <- reactive({
             req(single_assay())
@@ -104,12 +104,15 @@ server_module_pca_box <- function(id, single_assay, method, transpose) {
             return(df)
         })
 
+
         pca_result <- reactive({
             req(single_assay())
             pcaMethods_wrapper(
                 single_assay(),
                 method = method,
-                transpose = transpose
+                transpose = transpose,
+                scale = input$scale,
+                center = input$center
             )
         })
         dataframe <- reactive({

R/server_module_summary_tab.R

@@ -62,7 +62,7 @@ server_module_summary_tab <- function(id) {
 
         output$download_qfeatures <- downloadHandler(
             filename = function() {
-                "scp_qfeature_object.rds"
+                "qfeatures_object.rds"
             },
             content = function(file) {
                 saveRDS(global_rv$qfeatures, file)

R/utils_global.R

@@ -166,6 +166,8 @@ remove_scpGUI <- function(string) {
 #'
 #' @param sce A SingleCellExperiment object. The PCA is performed on the assay of this object.
 #' @param method A character string specifying the PCA method to use. This should be one of the methods supported by the pcaMethods package.
+#' @param center A logical indicating whether the variables should be centered before PCA.
+#' @param scale A logical indicating whether the variables should be scaled before PCA.
 #'
 #' @return A pcaRes object resulting from the PCA.
 #' @rdname INTERNAL_pcaMethods_wrapper
@@ -174,15 +176,19 @@ remove_scpGUI <- function(string) {
 #' @importFrom pcaMethods pca
 #' @importFrom SummarizedExperiment assay
 #'
-pcaMethods_wrapper <- function(sce, method, transpose = FALSE) {
+pcaMethods_wrapper <- function(sce, method, center, scale, transpose = FALSE) {
     mat <- assay(sce)
     mat <- mat[rowSums(is.na(mat)) != ncol(mat), ]
     mat <- mat[, colSums(is.na(mat)) < nrow(mat)]
+    if (scale) {
+        mat <- scale(mat)
+    }
     if (transpose) {
         mat <- t(mat)
     }
     pca <- pcaMethods::pca(mat,
-        method = method
+        method = method,
+        center = center
     )
     pca
 }