Switched file reads to data.table::fread

DESCRIPTION

@@ -42,5 +42,5 @@ biocViews: ImmunoOncology, MassSpectrometry, Proteomics, Software, ShinyApps,
 BugReports: https://github.com/Vitek-Lab/MSstatsShiny/issues
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.3
 Config/testthat/edition: 3
+Config/roxygen2/version: 8.0.0

NAMESPACE

@@ -218,9 +218,6 @@ importFrom(tools,file_ext)
 importFrom(utils,capture.output)
 importFrom(utils,head)
 importFrom(utils,packageVersion)
-importFrom(utils,read.csv)
-importFrom(utils,read.delim)
-importFrom(utils,read.table)
 importFrom(utils,txtProgressBar)
 importFrom(utils,write.csv)
 importFrom(utils,write.table)

R/MSstatsShiny.R

@@ -39,7 +39,7 @@
 #' @importFrom MSstatsPTM dataProcessPlotsPTM groupComparisonPlotsPTM MaxQtoMSstatsPTMFormat PDtoMSstatsPTMFormat FragPipetoMSstatsPTMFormat SkylinetoMSstatsPTMFormat MetamorpheusToMSstatsPTMFormat SpectronauttoMSstatsPTMFormat
 #' @importFrom MSstatsBioNet exportNetworkToHTML deleteEdgeFromNetwork
 #' @importFrom MSstatsResponse futureExperimentSimulation run_tpr_simulation plot_tpr_power_curve calculateTurnoverRatios
-#' @importFrom utils capture.output head packageVersion read.csv read.delim write.csv
+#' @importFrom utils capture.output head packageVersion write.csv
 #' @importFrom stats aggregate
 #' @importFrom methods is
 #' @importFrom readxl read_excel

R/module-loadpage-server.R

@@ -187,7 +187,7 @@ loadpageServer <- function(id, parent_session, is_web_server = FALSE, app_templa
         ui_elements <- tagList(ui_elements, create_spectronaut_standard_ui(session$ns))
       }
 
-      tagList(ui_elements, create_separator_buttons(session$ns, "sep_specdata"))
+      ui_elements
     })
 
     output$spectronaut_turnover_ui <- renderUI({
@@ -305,7 +305,6 @@ loadpageServer <- function(id, parent_session, is_web_server = FALSE, app_templa
     #   enable("proceed1")
     # })
 
-    # can remove separator is.null check because shiny by default assigns the first value as the default value for radiobutton
     observe({
       disable("proceed1")
       if(((input$BIO == "Protein") || (input$BIO == "Peptide"))) {
@@ -316,38 +315,37 @@ loadpageServer <- function(id, parent_session, is_web_server = FALSE, app_templa
                 enable("proceed1")
               }
             } else if (input$filetype == "msstats") {
-              if(!is.null(input$msstatsdata) && !is.null(input$sep_msstatsdata)) {
+              if(!is.null(input$msstatsdata)) {
                 enable("proceed1")
               }
             } else if (input$filetype == "sky") {
-              print(input$sep_skylinedata)
-              if(!is.null(input$skylinedata) && !is.null(input$sep_skylinedata)) { # && !is.null(input$annot)
+              if(!is.null(input$skylinedata)) {
                 enable("proceed1")
               }
             } else if (input$filetype == "maxq") {
               if(!is.null(input$evidence) && !is.null(input$pGroup)) { # && !is.null(input$annot1)
                 enable("proceed1")
               }
             } else if (input$filetype == "prog" || input$filetype == "PD" || input$filetype == "open" || input$filetype == "phil" || input$filetype == "meta") {
-              if(!is.null(input$data) && !is.null(input$sep_data)) { # && !is.null(input$annot)
+              if(!is.null(input$data)) {
                 enable("proceed1")
               }
             } else if (input$filetype == "openms") {
-              if(!is.null(input$data) && !is.null(input$sep_data)) {
+              if(!is.null(input$data)) {
                 enable("proceed1")
               }
             } else if (input$filetype == "spec") {
               spec_regular_file_ok <- !isTRUE(input$big_file_spec) && !is.null(input$specdata)
               spec_big_file_ok <- isTRUE(input$big_file_spec) && length(local_big_file_path()) > 0
-              if((spec_regular_file_ok || spec_big_file_ok) && !is.null(input$sep_specdata)) {
+              if(spec_regular_file_ok || spec_big_file_ok) {
                 enable("proceed1")
               }
             } else if (input$filetype == "ump") {
               if(!is.null(input$fragSummary) && !is.null(input$peptideSummary) && !is.null(input$protSummary)) {  #&& !is.null(input$annot2)
                 enable("proceed1")
               }
             } else if (input$filetype == "diann") {
-              if(!is.null(input$dianndata) && !is.null(input$sep_dianndata)) { # && !is.null(input$annot)
+              if(!is.null(input$dianndata)) {
                 enable("proceed1")
               }
             }
@@ -362,29 +360,29 @@ loadpageServer <- function(id, parent_session, is_web_server = FALSE, app_templa
                 enable("proceed1")
               }
             } else if (input$filetype == "PD") {
-              if(!is.null(input$data) && !is.null(input$sep_data)) { # && !is.null(input$annot)
+              if(!is.null(input$data)) {
                 enable("proceed1")
               }
             } else if (input$filetype == "openms") {
-              if(!is.null(input$data) && !is.null(input$sep_data)) {
+              if(!is.null(input$data)) {
                 enable("proceed1")
               }
             } else if (input$filetype == "spmin" || input$filetype == "phil") {
-              if(!is.null(input$data) && !is.null(input$sep_data)) { # && !is.null(input$annot)
+              if(!is.null(input$data)) {
                 enable("proceed1")
               }
             }
           }
         }
-        
+
       }
       else if ((input$BIO == "PTM")) {
         if (input$DDA_DIA == "LType" || input$DDA_DIA == "TMT") {
           if ((!is.null(input$filetype) && length(input$filetype) > 0)) {
             if (input$filetype == "sample") {
               enable("proceed1")
             } else if (input$filetype == "msstats") {
-              if(!is.null(input$msstatsptmdata) && !is.null(input$sep_msstatsptmdata)) {
+              if(!is.null(input$msstatsptmdata)) {
                 enable("proceed1")
               }
             } else if (input$filetype == "sky" || input$filetype == "maxq" || input$filetype == "spec" || input$filetype == "PD" || input$filetype == "meta") {

R/module-loadpage-ui.R

@@ -215,8 +215,7 @@ create_standard_uploads <- function(ns) {
     condition = "(input['loadpage-filetype'] =='10col' || input['loadpage-filetype'] =='prog' || input['loadpage-filetype'] =='PD' || input['loadpage-filetype'] =='open'||
                    input['loadpage-filetype'] =='openms' || input['loadpage-filetype'] =='spmin' || input['loadpage-filetype'] == 'phil' || input['loadpage-filetype'] == 'meta') && input['loadpage-BIO'] != 'PTM'",
     h4("4. Upload quantification dataset"),
-    fileInput(ns('data'), "", multiple = FALSE, accept = NULL),
-    create_separator_buttons(ns, "sep_data")
+    fileInput(ns('data'), "", multiple = FALSE, accept = NULL)
   )
 }
 
@@ -240,17 +239,15 @@ create_msstats_uploads <- function(ns) {
     conditionalPanel(
       condition = "input['loadpage-filetype'] == 'msstats' && (input['loadpage-BIO'] != 'PTM' && (input['loadpage-BIO'] != 'PTM' && input['loadpage-DDA_DIA'] != 'TMT'))",
       h4("4. Upload data in MSstats Format"),
-      fileInput(ns('msstatsdata'), "", multiple = FALSE, accept = NULL),
-      create_separator_buttons(ns, "sep_msstatsdata")
+      fileInput(ns('msstatsdata'), "", multiple = FALSE, accept = NULL)
     ),
 
     # PTM MSstats format
     conditionalPanel(
       condition = "input['loadpage-filetype'] == 'msstats' && (input['loadpage-BIO'] == 'PTM' || (input['loadpage-BIO'] == 'PTM' && input['loadpage-DDA_DIA'] == 'TMT'))",
       h4("4. Upload PTM data in MSstats Format"),
       fileInput(ns('msstatsptmdata'), "", multiple = FALSE, accept = NULL),
-      create_separator_buttons(ns, "sep_msstatsptmdata"),
-
+
       h4("5. (Optional) Upload unmodified data in MSstats Format"),
       fileInput(ns('unmod'), "", multiple = FALSE, accept = NULL),
       tags$br()
@@ -264,8 +261,7 @@ create_skyline_uploads <- function(ns) {
   conditionalPanel(
     condition = "input['loadpage-filetype'] == 'sky' && input['loadpage-BIO'] != 'PTM'",
     h4("4. Upload MSstats report from Skyline"),
-    fileInput(ns('skylinedata'), "", multiple = FALSE, accept = NULL),
-    create_separator_buttons(ns, "sep_skylinedata")
+    fileInput(ns('skylinedata'), "", multiple = FALSE, accept = NULL)
   )
 }
 
@@ -275,8 +271,7 @@ create_diann_uploads <- function(ns) {
   conditionalPanel(
     condition = "input['loadpage-filetype'] == 'diann' && input['loadpage-BIO'] != 'PTM'",
     h4("4. Upload MSstats report from DIANN"),
-    fileInput(ns('dianndata'), "", multiple = FALSE, accept = NULL),
-    create_separator_buttons(ns, "sep_dianndata")
+    fileInput(ns('dianndata'), "", multiple = FALSE, accept = NULL)
   )
 }
 
@@ -664,19 +659,3 @@ create_quality_filtering_options <- function(ns) {
     )
   )
 }
-
-
-#' Create column separator radio buttons
-#' 
-#' @param ns Namespace function
-#' @param input_id ID for the radio button input
-#' @noRd
-create_separator_buttons <- function(ns, input_id) {
-  radioButtons(ns(input_id),
-               label = h5("Column separator in uploaded file", class = "icon-wrapper", 
-                          icon("question-circle", lib = "font-awesome"),
-                          div("Choose how columns are separated in the uploaded file", class = "icon-tooltip")),
-               c(Comma=",", Semicolon=";", Tab="\t", Pipe="|"),
-               inline = TRUE
-  )
-}

R/module-visualize-network-server.R

@@ -111,7 +111,7 @@ loadCsvData <- function(input, dataComparison) {
   }
   req(input$dataUpload)
   tryCatch({
-    read.csv(input$dataUpload$datapath)
+    data.table::fread(input$dataUpload$datapath)
   }, error = function(e) {
     showNotification(paste("Error reading file:", e$message), type = "error")
     return(NULL)
@@ -535,7 +535,7 @@ visualizeNetworkServer <- function(id, parent_session, dataComparison) {
     codes <- paste(codes, "library(MSstatsBioNet)\nlibrary(dplyr)\n\n", sep = "")
 
     codes <- paste(codes, "# Read data\n", sep = "")
-    codes <- paste(codes, "df <- read.csv(\"path/to/your/data.csv\")\n\n", sep = "")
+    codes <- paste(codes, "df <- data.table::fread(\"path/to/your/data.csv\")\n\n", sep = "")
 
     # Add label filtering if not default
     if (params$selectedLabel != "" && !is.null(params$selectedLabel)) {

R/plotting_funtions.R

@@ -82,7 +82,7 @@
 #' @importFrom grDevices dev.off pdf
 #' @importFrom graphics image mtext par plot.new
 #' @importFrom stats dist hclust qt
-#' @importFrom utils read.table write.table
+#' @importFrom utils write.table
 #' 
 #' @examples
 #' data("dia_skyline_model")
@@ -136,7 +136,7 @@ groupComparisonPlots2 = function(data=data,
     }
 
     finalfile = lastfilename
-    processout = as.matrix(read.table(finalfile, header=TRUE, sep="\t"))
+    processout = as.matrix(data.table::fread(finalfile))
   }	
 
   processout = rbind(processout, as.matrix(c(" ", " ", "MSstats - groupComparisonPlots function", " "), ncol=1))