Plotly plots Design Experiments | MSstatsTMT Plotly plots adaptation for Shiny

R/module-expdes-server.R

@@ -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,
     })
   })
 
-}
+}

R/module-qc-server.R

@@ -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
     )
   )
-}
+}

R/module-qc-ui.R

@@ -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'),

R/module-statmodel-server.R

@@ -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)
       })