added renaming from template functionality

ParkerICI · Jan 12, 2022 · 89c5fee · 89c5fee
1 parent 735567e
commit 89c5fee
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Showing 2 changed files with 29 additions and 2 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: premessa
 Type: Package
 Title: R package for pre-processing of flow and mass cytometry data
-Version: 0.3.0
+Version: 0.3.1
 Author: "Pier Federico Gherardini <federico.gherardini@gmail.com> [aut, cre]"
 Description: This package includes panel editing/renaming for FCS files, bead-based normalization and debarcoding.
 Imports: shiny (>= 0.14), flowCore, reshape, ggplot2, hexbin, gridExtra, rhandsontable, jsonlite, data.table, shinyjqui

diff --git a/inst/paneleditor_shinyGUI/server.R b/inst/paneleditor_shinyGUI/server.R
@@ -7,6 +7,9 @@ render_paneleditor_ui <- function(working.directory, ...) {renderUI({
             column(6,
                 textInput("paneleditorui_output_folder", label = "Output folder name", value = "renamed")
             ),
+            column(3,
+                actionButton("paneleditorui_load_template", "Load template")
+            ),
             column(3,
                 actionButton("paneleditorui_process_files", "Process files")
             )
@@ -33,7 +36,19 @@ get_panel_table <- function(files.list) {
     return(panel.table)
 }
 
-
+rename_from_template <- function(tab, template.file.path) {
+    template <- read.csv(template.file.path, header = FALSE)
+    if(ncol(template) < 2)
+        stop("Template file format incorrect")
+    names.map <- setNames(template[, 2], template[, 1])
+    names.map <- names.map[names(names.map) %in% row.names(tab)]
+    fcs.cols <- grep("FCS$", names(tab), ignore.case = TRUE)
+    w.na <- is.na(tab[names(names.map), fcs.cols])
+    tab[names(names.map), fcs.cols] <- names.map
+    tab[names(names.map), fcs.cols][w.na] <- NA
+    tab[, "Most common"] <- premessa:::get_common_names(tab)
+    return(tab)
+}
 
 shinyServer(function(input, output, session) {
     working.directory <- dirname(file.choose())
@@ -80,6 +95,18 @@ shinyServer(function(input, output, session) {
     output$paneleditorui_panel_table <- rhandsontable::renderRHandsontable({
         temp <- panel.table
 
+        if(!is.null(input$paneleditorui_load_template) && input$paneleditorui_load_template != 0) {
+            temp <- tryCatch(rename_from_template(temp, file.choose()),
+                             error = function(cond) {
+                                 showModal(modalDialog(
+                                     title = "Panel editor error",
+                                     "Template file format incorrect. Should be a CSV with two columns:", br(),
+                                     "CHANNEL-NAME,PARAMETER-NAME"
+                                 ))
+                                 temp
+                             })
+        }
+
         for(i in 1:ncol(temp))
             temp[, i][is.na(temp[, i])] <- "absent"