@@ -1,7 +1,7 @@

 Package: MSstatsShiny

 Type: Package

 Title: MSstats GUI for Statistical Anaylsis of Proteomics Experiments

-Version: 1.6.0

+Version: 1.7.1

 Description: MSstatsShiny is an R-Shiny graphical user interface (GUI) 

   integrated with the R packages MSstats, MSstatsTMT, and MSstatsPTM. It 

   provides a point and click end-to-end analysis pipeline applicable to a wide 

@@ -48,54 +48,8 @@ expdesServer <- function(input, output, session,parent_session, loadpage_input,

                              power= power_x)

     }

-    #  plot output

-   designSampleSizePlots_ggplotly <- function(data) {

-  index <- if (length(unique(data$numSample)) > 1) {

-    "numSample"

-  } else if (length(unique(data$power)) > 1) {

-    "power"

-  } else if (length(unique(data$numSample)) == 1 & length(unique(data$power)) == 1) {

-    "numSample"

-  } else {

-    stop("Invalid input")

-  }

-  

-  text.size <- 12

-  axis.size <- 13

-  lab.size <- 17

-  

-  if (index == "numSample") {

-    p <- plot_ly(data, x = ~desiredFC, y = ~numSample, type = "scatter", mode = "lines")

-    p <- layout(p, xaxis = list(title = "Desired fold change"),

-                yaxis = list(title = "Minimal number of biological replicates"),

-                showlegend = TRUE,

-                annotations = list(text = paste("FDR is", unique(data$FDR),

-                                                "<br>Statistical power is", unique(data$power))),

-                font = list(size = text.size, family = "Arial"),

-                title = "")

-  }

-  

-  if (index == "power") {

-    p <- plot_ly(data, x = ~desiredFC, y = ~power, type = "scatter", mode = "lines")

-    p <- layout(p, xaxis = list(title = "Desired fold change"),

-                yaxis = list(title = "Power"),

-                showlegend = TRUE,

-                annotations = list(text = paste("Number of replicates is", unique(data$numSample),

-                                                "<br>FDR is", unique(data$FDR))),

-                font = list(size = text.size, family = "Arial"),

-                title = "")

-  }

-  

-  return(p)

-}

-

-    

-    

-    

-

-

     output$result_plot = renderPlotly({

-      designSampleSizePlots_ggplotly(future_exp())

+      designSampleSizePlots(future_exp(), isPlotly = TRUE)

     })

     #download

@@ -117,4 +71,4 @@ expdesServer <- function(input, output, session,parent_session, loadpage_input,

     })

   })

-}

\ No newline at end of file

+}

@@ -107,15 +107,15 @@ qcServer <- function(input, output, session,parent_session, loadpage_input,get_d

     print("Inside render UI and getting input$type1")

     print(input$type1)

     if ((loadpage_input()$BIO!="PTM" && input$type1 == "QCPlot")) {

-      if((loadpage_input()$DDA_DIA=="LType" && loadpage_input()$filetype=="sky") || (loadpage_input()$DDA_DIA=="LType" && loadpage_input()$filetype=="ump")){

-        selectizeInput(ns("which"), "Show plot for", 

-                       choices = c("", "ALL PROTEINS" = "allonly", 

-                                   unique(get_data()[2])))

-      } else {

-        selectizeInput(ns("which"), "Show plot for", 

-                       choices = c("", "ALL PROTEINS" = "allonly", 

-                                   unique(get_data()[1])))

-      }

+      # if((loadpage_input()$DDA_DIA=="LType" && loadpage_input()$filetype=="sky") || (loadpage_input()$DDA_DIA=="LType" && loadpage_input()$filetype=="ump")){

+      #   selectizeInput(ns("which"), "Show plot for", 

+      #                  choices = c("", "ALL PROTEINS" = "allonly", 

+      #                              unique(get_data()[2])))

+      # } else {

+      selectizeInput(ns("which"), "Show plot for", 

+                     choices = c("", "ALL PROTEINS" = "allonly", 

+                                 unique(get_data()[1])))

+      # }

     } else if (loadpage_input()$BIO == "PTM"){

       if (input$type1 == "QCPlot"){

         selectizeInput(ns("which"), "Show plot for", 

@@ -162,17 +162,17 @@ qcServer <- function(input, output, session,parent_session, loadpage_input,get_d

       # }

       if(loadpage_input()$DDA_DIA == "TMT"){

-        

-        dataProcessPlotsTMT(preprocess_data(),

+        plot <- dataProcessPlotsTMT(preprocess_data(),

                             type=input$type1,

+                            featureName = input$fname,

                             ylimUp = FALSE,

                             ylimDown = FALSE,

                             which.Protein = protein,

-                            originalPlot = TRUE,

+                            originalPlot = original,

                             summaryPlot = input$summ,

-                            address = file

-        )

-

+                            address = file, isPlotly = TRUE

+        )[[1]]

+        return(plot)

       } else if (loadpage_input()$BIO == "PTM"){

@@ -370,8 +370,8 @@ qcServer <- function(input, output, session,parent_session, loadpage_input,get_d

   output$showplot = renderUI({

     ns<- session$ns

-    # TMT and PTM plotly plots are still under development

-    if ((loadpage_input()$DDA_DIA == "TMT") || (loadpage_input()$BIO == "PTM")) {

+    # PTM plotly plots are still under development

+    if (loadpage_input()$BIO == "PTM") {

       output$theplot = renderPlot(theplot())

       op <- plotOutput(ns("theplot"))

     } else {

@@ -491,4 +491,4 @@ qcServer <- function(input, output, session,parent_session, loadpage_input,get_d

       preprocessData = preprocess_data

     )

   )

-}

\ No newline at end of file

+}

@@ -236,7 +236,7 @@ qcUI <- function(id) {

                           #                  tags$br(),

                           #                  tags$h4("Calculation in progress...")),

                           uiOutput(ns("showplot")),

-                          disabled(downloadButton(ns("saveplot"), "Save this plot"))

+                          # disabled(downloadButton(ns("saveplot"), "Save this plot"))

                  ),

                  tabPanel("Download Data", 

                           #verbatimTextOutput('effect'),

@@ -411,18 +411,20 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu

     } else if(loadpage_input()$DDA_DIA=="TMT"){

       tryCatch({

-        plot1 = MSstatsShiny::groupComparisonPlots2(data=data_comparison()$ComparisonResult,

-                                                    type=input$typeplot,

-                                                    sig=input$sig,

-                                                    FCcutoff=input$FC,

-                                                    logBase.pvalue=input$logp,

-                                                    ProteinName=input$pname,

-                                                    numProtein=input$nump, 

-                                                    clustering=input$cluster, 

-                                                    which.Comparison=input$whichComp,

-                                                    which.Protein = input$whichProt,

-                                                    address=path1(),

-                                                    savePDF=pdf)

+        # makes use of MSstats groupComparisonPlots function

+        plot1 = groupComparisonPlots(data=data_comparison()$ComparisonResult,

+                                     type=input$typeplot,

+                                     sig=input$sig,

+                                     FCcutoff=input$FC,

+                                     logBase.pvalue=as.numeric(input$logp),

+                                     ProteinName=input$pname,

+                                     numProtein=input$nump, 

+                                     clustering=input$cluster, 

+                                     which.Comparison=input$whichComp,

+                                     which.Protein = input$whichProt,

+                                     height = input$height,

+                                     address="Ex_",

+                                     isPlotly = TRUE)[[1]]

       remove_modal_spinner()

       },

       error = function(e){

@@ -715,8 +717,8 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu

   observeEvent(input$viewresults, {

     ns <- session$ns

-    # TMT and PTM plotly plots are still under development

-    if ((loadpage_input()$DDA_DIA == "TMT") || (loadpage_input()$BIO == "PTM")) {

+    # PTM plotly plots are still under development

+    if (loadpage_input()$BIO == "PTM") {

       output$comp_plots = renderPlot({

         group_comparison(FALSE, FALSE)

       })