@@ -23,7 +23,7 @@ Authors@R: c(

     person("Olga", "Vitek", email = "[email protected]", role = "aut"))

 License: Artistic-2.0

 Depends: R (>= 4.2)

-Imports: shiny, shinyBS, shinyjs, shinybusy, dplyr, ggplot2, data.table, Hmisc,

+Imports: shiny, shinyBS, shinyjs, shinybusy, dplyr, ggplot2,plotly, data.table, Hmisc,

   MSstats, MSstatsTMT, MSstatsPTM, MSstatsConvert, gplots, marray, DT, readxl,

   ggrepel, uuid, utils, stats, htmltools, methods, tidyr, grDevices, graphics

 Suggests: 

@@ -15,6 +15,10 @@ import(MSstatsConvert)

 import(MSstatsTMT)

 import(data.table)

 import(ggplot2)

+importFrom(plotly,plot_ly)

+importFrom(plotly,ggplotly)

+importFrom(plotly,plotlyOutput)

+importFrom(plotly,renderPlotly)

 importFrom(DT,dataTableOutput)

 importFrom(DT,renderDataTable)

 importFrom(Hmisc,describe)

@@ -436,6 +436,7 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu

                                                             savePDF=pdf)

       }, error = function(e){

         remove_modal_spinner()

+        message("An error occurred: ", conditionMessage(e))

         stop( '** Cannnot generate multiple plots in a screen. Please refine selection or save to a pdf.**' )}

       )

     }

@@ -677,7 +678,7 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu

     insertUI(

       selector = paste0("#", ns("comparison_plots")),

       ui=tags$div(

-        plotOutput(ns("comp_plots"), height = "100%", click = "click1"),

+        plotlyOutput(ns("comp_plots"), height = "100%"),

         conditionalPanel(condition = "input['statmodel-typeplot'] == 'VolcanoPlot' && input['loadpage-DDA_DIA']!='TMT'",

                          h5("Click on plot for details"),

                          verbatimTextOutput(ns("info2"))),

@@ -688,8 +689,9 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu

   }

   )

-  observe({output$comp_plots = renderPlot({

-    group_comparison(FALSE, FALSE)}, height = input$height

+  observe({output$comp_plots = renderPlotly({

+    group_comparison(FALSE, FALSE)

+    }

   )

   })

@@ -847,6 +849,7 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu

     }

   )

+  

   output$plotresults = downloadHandler(

     filename = function() {

       paste("SummaryPlot-", Sys.Date(), ".pdf", sep="")

@@ -118,58 +118,58 @@ groupComparisonPlots2 = function(data=data,

   allfiles = list.files()

   filenaming = "msstats"

   if (length(grep(filenaming,allfiles)) == 0) {

-

+    

     finalfile = "msstats.log"

     processout = NULL

-

+    

   } else {

-

+    

     num = 0

     finalfile = "msstats.log"

-

+    

     while(is.element(finalfile, allfiles)) {

       num = num + 1

       lastfilename = finalfile ## in order to rea

       finalfile = paste(paste(filenaming, num, sep="-"), ".log", sep="")

     }

-

+    

     finalfile = lastfilename

     processout = as.matrix(read.table(finalfile, header=TRUE, sep="\t"))

   }

-

+  

   processout = rbind(processout, as.matrix(c(" ", " ", "MSstats - groupComparisonPlots function", " "), ncol=1))

-

+  

   ## make upper letter

   type = toupper(type)

-

+  

   if (length(setdiff(type, c("HEATMAP", "VOLCANOPLOT", "COMPARISONPLOT"))) != 0) {

-

+    

     processout = rbind(processout, c(paste("Input for type=", type, ". However,'type' should be one of \"Heatmap\", \"VolcanoPlot\",\"ComparisonPlot\".", sep="")))

     write.table(processout, file=finalfile, row.names=FALSE)

-

+    

     stop(paste("Input for type=", type, ". However,'type' should be one of \"Heatmap\", \"VolcanoPlot\",\"ComparisonPlot\".", sep=""))

   }

-

+  

   ## check logBase.pvalue is 2,10 or not

   if (logBase.pvalue != 2 & logBase.pvalue != 10) {

     processout = rbind(processout, c("ERROR : (-) Logarithm transformation for adjusted p-values : log2 or log10 only - stop"))

     write.table(processout, file=finalfile, row.names=FALSE)

-

+    

     stop("Only -log2 or -log10 for logarithm transformation for adjusted p-values are posssible.\n")

   }

-

+  

   if (which.Comparison != "all") {

     ## check which.comparison is name of comparison

     if (is.character(which.Comparison)) {

-

+      

       temp.name = which.Comparison

-

+      

       ## message if name of comparison is wrong.

       if (length(setdiff(temp.name, unique(data$Label))) > 0) {

-

+        

         processout = rbind(processout, paste("Please check labels of comparions. Result does not have this comparison. -", paste(temp.name, collapse=", "), sep=" "))

         write.table(processout, file=finalfile, row.names=FALSE)

-

+        

         stop(paste("Please check labels of comparions. Result does not have this comparison. -", paste(temp.name, collapse=", "), sep=" "))

       }

     }

@@ -399,7 +399,7 @@ groupComparisonPlots2 = function(data=data,

         }

       } else if ( length(which.Comparison) > 1 ) {

         stop( '** Cannnot generate multiple volcano plots in a screen. Please set one comparison at a time.' )

-

+        

       }

     }

@@ -761,9 +761,9 @@ groupComparisonPlots2 = function(data=data,

         print(ptemp)

       }

       else {

-        return(ptemp)

+        return(ggplotly(ptemp))

       }

-

+      

     } ## end-loop

     # if (address!=FALSE) {

@@ -788,7 +788,7 @@ groupComparisonPlots2 = function(data=data,

         stop( '** Cannnot generate multiple comparison plots in a screen. Please set one protein at a time.' )

       }

     }

-

+    

     ## choose Proteins or not

     if (which.Protein != "all") {

       ## check which.Protein is name of Protein

@@ -887,7 +887,7 @@ groupComparisonPlots2 = function(data=data,

         print(ptemp)

       }

       else {

-        return(ptemp)

+        return(ggplotly(ptemp))

       }

       message(paste("Drew compasison plot for ", unique(sub$PROTEIN), "(", i, " of ", length(unique(datatemp$Protein)), ")"))