srv_GO_enrichment.R
In Prostar: Provides a GUI for DAPAR

callModule(moduleProcess, "moduleProcess_GO", 
           isDone = reactive({rvModProcess$moduleGODone}), 
           pages = reactive({rvModProcess$moduleGO}),
           rstFunc = resetModuleGO,
           forceReset = reactive({rvModProcess$moduleGOForceReset })  )



resetModuleGO <- reactive({  
  ## update rv$widgets values (reactive values)
  resetModuleProcess("GO")
  
  rv$widgets$go$sourceOfProtID <- NULL
  rv$widgets$go$idFrom <- "UNIPROT"
  rv$widgets$go$Organism <- character(0)
  rv$widgets$go$Ontology <- character(0)
  rv$widgets$go$UniprotIDCol <- character(0)
  rv$widgets$go$UNIPROTID_File <- NULL
  rv$widgets$go$GO_level <- 2
  rv$widgets$go$universe <- NULL
  rv$widgets$go$UniverseFile <- NULL
  rv$widgets$go$pvalueCutoff <- 0.01
  
  rv$widgets$go$ProtIDList=NULL
  rv$widgets$go$gene=NULL
  rv$widgets$go$proteinsNotMapped=NULL
  rv$widgets$go$ratio=NULL
  rv$widgets$go$uniprotID=NULL
  rv$widgets$go$universeData=NULL
  rv$widgets$go$enrichGO_data=NULL
  rv$widgets$go$groupGO_data=NULL
  
  
  rvModProcess$moduleGODone =  rep(FALSE,4)
})

##--------------------------------------------------------
##---------------------------------------------------------

observeEvent(input$sourceOfProtID,{  rv$widgets$go$sourceOfProtID <- input$sourceOfProtID})
observeEvent(input$idFrom,{  rv$widgets$go$idFrom <- input$idFrom})
observeEvent(input$Organism,{  rv$widgets$go$Organism <- input$Organism})
observeEvent(input$Ontology,{  rv$widgets$go$Ontology <- input$Ontology})
observeEvent(input$UniprotIDCol,{  rv$widgets$go$UniprotIDCol <- input$UniprotIDCol})
observeEvent(input$UNIPROTID_File,{  rv$widgets$go$UNIPROTID_File <- input$UNIPROTID_File})
observeEvent(input$GO_level,{  rv$widgets$go$GO_level <- input$GO_level})
observeEvent(input$universe,{  rv$widgets$go$universe <- input$universe})
observeEvent(input$UniverseFile,{  rv$widgets$go$UniverseFile <- input$UniverseFile})
observeEvent(input$pvalueCutoff,{  rv$widgets$go$pvalueCutoff <- input$pvalueCutoff})

observeEvent(rvModProcess$moduleGoForceReset,{
  rv$widgets$go$UNIPROTID_File <- NULL
  rv$widgets$go$UniverseFile <- NULL
})


output$resettableUniprotidFile <- renderUI({
  rv$widgets$go$UNIPROTID_File
  tagList(
    p("Select file containing protein IDs"),
  fileInput("uniprotFile", rv$widgets$go$UNIPROTID_File$name)
  )
})

output$resettableUniverseFile <- renderUI({
  req(c(rv$widgets$go$UniverseFile, rv$widgets$go$universe))
  if (rv$widgets$go$universe == "Custom"){
    fileInput("UniverseFile", rv$widgets$go$UniverseFile$name, 
            multiple=FALSE) 
  }
})


output$screenGO1 <- renderUI({
  print("output$screenGO1 <- renderUI")
  tagList(
    tags$div(
      tags$div( style="display:inline-block; vertical-align: middle; padding-right: 20px;",
                radioButtons("sourceOfProtID", "Source of protein ID",
               choices = G_sourceOfProtID_Choices,
               selected = rv$widgets$go$sourceOfProtID_Choices)),
      tags$div( style="display:inline-block; vertical-align: middle; padding-right: 20px;",
                uiOutput("chooseSourceForProtID")),
      tags$div( style="display:inline-block; vertical-align: middle; padding-right: 20px;",
              selectInput("idFrom", "Id From", choices = c("UNIPROT", "ENTREZID"),
                          selected = rv$widgets$go$idFrom), width="200px"),
      tags$div( style="display:inline-block; vertical-align: middle; padding-right: 20px;",
              modulePopoverUI("modulePopover_GenomeWide"),
              selectInput("Organism", NULL, choices = GetListInstalledOrgdDB(),
                          selected=rv$widgets$go$Organism), width="200px"),
      tags$div( style="display:inline-block; vertical-align: middle; padding-right: 20px;",
              selectInput("Ontology", "Ontology",choices = G_ontology_Choices,
                          selected = rv$widgets$go$Ontology), width="150px")
    ),
  actionButton("mapProtein.GO.button","Map proteins IDs", class = actionBtnClass),
  uiOutput("warnDifferentSizeID"),
  tags$hr(),
  uiOutput("infoIDProt_NA"),
  br(), br(),
  uiOutput("GeneMappedRatio"),
  br(), br(),
  if (nrow(pData(rv$current.obj))>153) p("The size of the table is too big to be exported with the buttons below (only the first 154 rows will be exported). It is advised to use the Export tool of Prostar."),
  DT::dataTableOutput("nonIdentifiedProteins", width = "80%")
  
)

})




output$screenGO2 <- renderUI({
  
  tagList(
  tags$div(
    tags$div( style="display:inline-block; vertical-align: middle;",
              modulePopoverUI("modulePopover_GOlevel"),
              checkboxGroupInput("GO_level", NULL,choices =c(2:4), selected=rv$widgets$go$GO_level)),
    tags$div( style="display:inline-block; vertical-align: middle; padding-right: 20px;",
              actionButton("group.GO.perform.button","Perform GO grouping", class = actionBtnClass))
  ),
  tags$hr(),

  withProgress(message = 'Building plot',detail = '', value = 0, {
    incProgress(1/3, detail = 'Goup level 2')
    highchartOutput("GOplotGroup_level2",  width = "80%")
    incProgress(2/3, detail = 'Goup level 3')
  highchartOutput("GOplotGroup_level3",  width = "80%")
  incProgress(3/3, detail = 'Goup level 4')
  highchartOutput("GOplotGroup_level4",  width = "80%")
  })
  
)
})



output$screenGO3 <- renderUI({
  tagList(
    tags$div(
      tags$div( style="display:inline-block; vertical-align: middle; padding-right: 20px;",
                modulePopoverUI("modulePopover_GOuniverse"),
                radioButtons("universe", NULL, choices = G_universe_Choices,
                             selected = rv$widgets$go$universe)
                ),
      tags$div( style="display:inline-block; vertical-align: middle; padding-right: 20px;",
                uiOutput("resettableUniverseFile")),
  # selectInput("PAdjustMethod", "P Adjust Method",choices = G_pAdjustMethod_Choices),
  tags$div( style="display:inline-block; vertical-align: middle; padding-right: 20px;",
            modulePopoverUI("modulePopover_GOfdr"),
            numericInput("pvalueCutoff", NULL, min = 0, max = 1, step = 0.01, 
                         value = rv$widgets$go$pvalueCutoff, width='100px'))
  ),
  
  actionButton("perform.GO.button","Perform enrichment analysis", class = actionBtnClass),
  tags$hr(),
  withProgress(message = 'Building plot',detail = '', value = 0, {
    incProgress(1/3, detail = 'Bar plot')
    highchartOutput("GObarplotEnrich", width = "80%")
    incProgress(1/3, detail = 'Dotplot')
    highchartOutput("GOdotplotEnrich", width = "80%")
  })
)
})


output$screenGO4 <- renderUI({
  
  DT::dataTableOutput("GO_resumeParams")
  
})




callModule(modulePopover,"modulePopover_GOlevel", 
           data = reactive(list(title = HTML(paste0("<strong>Level</strong>")), 
                                content="Level")))


callModule(modulePopover,"modulePopover_GOuniverse", 
           data = reactive(list(title = HTML(paste0("<strong>Universe</strong>")), 
                                content="universe")))
callModule(modulePopover,"modulePopover_GOfdr", 
           data = reactive(list(title = HTML(paste0("<strong>FDR</strong>")), 
                                content="BH Adjusted P-value cutoff")))



callModule(modulePopover,"modulePopover_GenomeWide", 
           data = reactive(list(title = HTML(paste0("<strong>Genome Wide Annotation</strong>")), 
                                content=paste0(tags$p("If the expected annotation database is not proposed in the dropdown menu, please find "),
                                               tags$a("here", href = "http://bioconductor.org/packages/release/BiocViews.html#___OrgDb",target="_blank"),
                                               tags$p(" the corresponding package. Then, install it (or have it installed by the administrator of the ProStaR server) and restart ProStaR.")))))



GetListInstalledOrgdDB <- function(){
  l <- installed.packages()[,"Package"]
  l <- l[grep("^org.", l)]
  res <-  list_org_db[l,]$longName
  names(l) <- res
  
  names(l)[which(is.na(names(l)))] <- l[which(is.na(names(l)))]
  
  return(l)
}


GetDataIndexForAnalysis <- reactive({
    req(rv$current.obj)
    
    index <- NULL
    if ("Significant" %in% names(Biobase::fData(rv$current.obj) )){
        index <- which(Biobase::fData(rv$current.obj)$Significant == TRUE)
    }else{
        index <- seq(1:nrow(rv$current.obj))
    }
    
    return(index)
})



output$chooseSourceForProtID <- renderUI({
    req(rv$current.obj)
    req(rv$widgets$go$sourceOfProtID)
    
    if (rv$widgets$go$sourceOfProtID == "colInDataset"){
        selectInput("UniprotIDCol", "Protein IDs",
                    choices = c("", colnames(Biobase::fData(rv$current.obj))),
                    selected = rv$widgets$go$UniprotIDCol)
    }
    else  if (rv$widgets$go$sourceOfProtID == "extFile"){
      uiOutput("resettableUniprotidFile")
    }
})








observeEvent(req(rv$widgets$go$UniprotIDCol),ignoreInit =  TRUE,{ 
    if((rv$widgets$go$UniprotIDCol == "")) {  rv$widgets$go$ProtIDList <- return (NULL)}
    else {
        rv$widgets$go$ProtIDList <- Biobase::fData(rv$current.obj)[,rv$widgets$go$UniprotIDCol]
    }
})


observeEvent(rv$widgets$go$UNIPROTID_File,ignoreInit =  TRUE,{ 
    rv$widgets$go$ProtIDList <- read.table(rv$widgets$go$UNIPROTID_File$datapath, header = FALSE, stringsAsFactors = FALSE)$V1
})


output$warnDifferentSizeID <- renderUI({
    req(rv$widgets$go$ProtIDList)
     if (length(rv$widgets$go$ProtIDList) != nrow(rv$current.obj)){
        h4("Warning : the protein ID list has not the same number of entites as the dataset.")
        br()
        h4("Please select another list of ID")
    }
})


observeEvent(input$mapProtein.GO.button,ignoreInit =  TRUE,{
  print("IN MAP button")
    req(rv$widgets$go$UniprotIDCol)
    rv$widgets$go$Organism
    rv$widgets$go$idFrom
    
    if(rv$widgets$go$UniprotIDCol == "") {  
        print("toto")
      rv$widgets$go$ProtIDList <- NULL
        return (NULL)}
    
    require(clusterProfiler)
    isolate({
        rv$widgets$go$gene <- NULL
        rv$widgets$go$ProtIDList <- Biobase::fData(rv$current.obj)[,rv$widgets$go$UniprotIDCol]
        index <- GetDataIndexForAnalysis()
        
        tryCatch({
            
             rv$widgets$go$gene <- bitr(rv$widgets$go$ProtIDList[index], fromType=rv$widgets$go$idFrom, toType="ENTREZID", OrgDb=rv$widgets$go$Organism)
            rv$widgets$go$proteinsNotMapped <- which((rv$widgets$go$ProtIDList[index] %in% rv$widgets$go$gene[,rv$widgets$go$idFrom]) == FALSE)
            rv$widgets$go$ratio <- 100*length(rv$widgets$go$proteinsNotMapped) / length(index)
            rvModProcess$moduleGODone[1] <- TRUE
        }, warning = function(w) {
            rv$widgets$go$gene <- bitr(rv$widgets$go$ProtIDList[index], fromType=rv$widgets$go$idFrom, toType="ENTREZID", OrgDb=rv$widgets$go$Organism)
            rv$widgets$go$proteinsNotMapped <- which((rv$widgets$go$ProtIDList[index] %in% rv$widgets$go$gene[,rv$widgets$go$idFrom]) == FALSE)
            rv$widgets$go$ratio <- 100*length(rv$widgets$go$proteinsNotMapped) / length(index)
            rvModProcess$moduleGODone[1] <- TRUE
            
        }, error = function(e) {
            # shinyjs::info(paste("Perform GO enrichment",":",conditionMessage(e), sep=" "))
            rv$widgets$go$ratio <- 100
        }, finally = {    
        }
        )
        
        
    })
})


##' Reactive behavior : GO analysis of data
##' @author Samuel Wieczorek
observeEvent(input$perform.GO.button,ignoreInit =  TRUE,{
    rv$widgets$go$universe
    rv$widgets$go$Organism
    rv$widgets$go$Ontology
    rv$widgets$go$pvalueCutoff
    req(rv$widgets$go$ProtIDList)
    rv$widgets$go$idFrom
    rv$widgets$go$uniprotID
   # req(rv$widgets$go$perform.GO.button)
  req(rv$widgets$go$ratio)
  
  print(rv$widgets$go$ratio)
    if (rv$widgets$go$ratio == 100){return(NULL)}
    
    require(clusterProfiler)
    
  withProgress(message = '',detail = '', value = 0, {
    incProgress(0.2, detail = 'Get universe data')
    
    if (rv$widgets$go$universe == "Entire dataset") {
        rv$widgets$go$universeData  <- rv$widgets$go$ProtIDList
    } else if (rv$widgets$go$universe == "Entire organism") {
        rv$widgets$go$universeData = DAPAR::univ_AnnotDbPkg(rv$widgets$go$Organism)
    } else {
        rv$widgets$go$universeData <- read.table(rv$widgets$go$UniverseFile$datapath, header = FALSE, stringsAsFactors = FALSE)
    }
    
    incProgress(0.4, detail = 'Get data to analyze')
    index <- GetDataIndexForAnalysis()
    incProgress(1, detail = 'Computing enrichment')
    rv$widgets$go$enrichGO_data <- enrich_GO(rv$widgets$go$ProtIDList[index],
                                  idFrom = rv$widgets$go$idFrom, 
                                  orgdb = rv$widgets$go$Organism, 
                                  ont = rv$widgets$go$Ontology, 
                                  pval = rv$widgets$go$pvalueCutoff, 
                                  universe = rv$widgets$go$universeData )
  })
  rvModProcess$moduleGODone[3] <- TRUE
})





observeEvent(input$group.GO.perform.button, ignoreInit =  TRUE,{
    rv$widgets$go$Organism
    rv$widgets$go$Ontology
    req(rv$widgets$go$ProtIDList)
    rv$widgets$go$uniprotID
    rv$widgets$go$idFrom
    rv$widgets$go$GO_level
    req(rv$widgets$go$ratio)
    
    if (rv$widgets$go$ratio == 100){return(NULL)}
    levelIndex <- sort(rv$widgets$go$GO_level)
    
    withProgress(message = '',detail = '', value = 0, {
      incProgress(1/(1+length(levelIndex)), detail = 'Get data for analysis')
      
    index <- GetDataIndexForAnalysis()
    rv$widgets$go$groupGO_data <- list()
    for (i in 1:length(levelIndex)){
      incProgress(1/(1+i), detail = paste0('Building plot for level ', i))
      rv$widgets$go$groupGO_data[[i]] <- list(level = as.numeric(levelIndex[i]),
                                     ggo_res = group_GO(rv$widgets$go$ProtIDList[index],
                                                        idFrom = rv$widgets$go$idFrom,
                                                        orgdb = rv$widgets$go$Organism,
                                                        ont=rv$widgets$go$Ontology,
                                                        level=as.numeric(levelIndex[i])))
    }
    })
    rvModProcess$moduleGODone[2] <- TRUE
    
})


##########################################
GOplotGroup_level2 <- reactive({
    req(rv$widgets$go$groupGO_data)
    
    isolate({
        if (length(rv$widgets$go$groupGO_data) >=1){
            barplotGroupGO_HC(rv$widgets$go$groupGO_data[[1]]$ggo_res, 
                              title = paste("Groups at level ", rv$widgets$go$groupGO_data[[1]]$level, sep=""))}
    })
})

##########################################
output$GOplotGroup_level2 <- renderHighchart({
    GOplotGroup_level2()
})


##########################################
GOplotGroup_level3 <- reactive({
    req(rv$widgets$go$groupGO_data)
    
    if ((length(rv$widgets$go$groupGO_data) < 2)){return(NULL)}
    isolate({
        barplotGroupGO_HC(rv$widgets$go$groupGO_data[[2]]$ggo_res, title = paste("Groups at level ",  rv$widgets$go$groupGO_data[[2]]$level))
    })
})


output$GOplotGroup_level3 <- renderHighchart({
    GOplotGroup_level3()
})

GOplotGroup_level4 <- reactive({
    req(rv$widgets$go$groupGO_data)
    
    if ((length(rv$widgets$go$groupGO_data) != 3)){return(NULL)}
    isolate({
            barplotGroupGO_HC(rv$widgets$go$groupGO_data[[3]]$ggo_res, title = paste("Groups at level ",  rv$widgets$go$groupGO_data[[3]]$level))
    })
})


output$GOplotGroup_level4 <- renderHighchart({
    GOplotGroup_level4()
})

GObarplotEnrich <- reactive({
    req(rv$widgets$go$enrichGO_data)
     barplotEnrichGO_HC(rv$widgets$go$enrichGO_data)
   
})

output$GObarplotEnrich <- renderHighchart({
    GObarplotEnrich()
    
})

GOdotplotEnrich <- reactive({
    req(rv$widgets$go$enrichGO_data)
    
    scatterplotEnrichGO_HC(rv$widgets$go$enrichGO_data)
})

output$GOdotplotEnrich <- renderHighchart({
    GOdotplotEnrich()
    
})


output$GODatatable <- renderDataTable(server=TRUE,{
    req(rv$widgets$go$enrichGO_data)
    req(rv$widgets$go$groupGO_data)
    
    
    dt <- DT::datatable( as.data.frame(rv$widgets$go$groupGO_data@result),
                     extensions = c('Scroller', 'Buttons'),
                     options = list(buttons = list('copy',
                                                   list(
                                                     extend = 'csv',
                                                     filename = 'GO_datatable'
                                                   ),'print'),
                                    dom='Bfrtip',
                                    initComplete = initComplete(),
                                    displayLength = 20,
                                    deferRender = TRUE,
                                    bLengthChange = FALSE,
                                    scrollX = 400,
                                    scrollY = 600,
                                    scroller = TRUE,
                                    ordering=FALSE,
                                    server = TRUE)
    )
    
    dt
})


output$GeneMappedRatio <- renderUI({
    req(rv$widgets$go$ProtIDList)
    req(rv$current.obj)
    req(rv$widgets$go$gene)
    rv$widgets$go$idFrom
    
    req(rv$widgets$go$ratio)
    
    index <- GetDataIndexForAnalysis()
    rv$widgets$go$proteinsNotMapped <- which((rv$widgets$go$ProtIDList[index] %in% rv$widgets$go$gene[,rv$widgets$go$idFrom]) == FALSE)
    nProtMapped <- length(rv$widgets$go$proteinsNotMapped)
    nProtTotal <-length(index)
    
    tagList(
        h5(paste(round(rv$widgets$go$ratio, digits=2), " % of the proteins have not been mapped (",nProtMapped," / ",nProtTotal,").", sep="")),
        helpText("These proteins are listed in the table below."),
        if (rv$widgets$go$ratio == 100){
            h3(paste("Tip: You should check the organism which has been selected.", sep=""))
        }
    )
})



output$Warning_nonIdentifiedProteins <- renderUI({
  GetDataFor_nonIdentifiedProteins()
  if (nrow(GetDataFor_nonIdentifiedProteins())>153) 
    p(MSG_WARNING_SIZE_DT)
  
})


GetDataFor_nonIdentifiedProteins <- reactive({
  req(rv$widgets$go$ProtIDList)
req(rv$current.obj)
req(rv$widgets$go$gene)
rv$widgets$go$idFrom

index <- GetDataIndexForAnalysis()
rv$widgets$go$proteinsNotMapped <- which((rv$widgets$go$ProtIDList[index] %in% rv$widgets$go$gene[,rv$widgets$go$idFrom]) == FALSE)
data <- as.data.frame(fData(rv$current.obj)[index[rv$widgets$go$proteinsNotMapped],])

data
}
)

output$nonIdentifiedProteins <- renderDataTable(server=TRUE,{
    req(rv$widgets$go$ProtIDList)
    req(rv$current.obj)
    req(rv$widgets$go$gene)
    rv$widgets$go$idFrom
    
    i
    data <- GetDataFor_nonIdentifiedProteins()
    if( nrow(data) != 0){
      
      dt <- DT::datatable( data,
                       extensions = c('Scroller', 'Buttons'),
                       options = list(buttons = list('copy',
                                                     list(
                                                       extend = 'csv',
                                                       filename = 'nonIdentifiedProteins'
                                                     ),'print'),
                                      dom='Bfrtip',
                                      initComplete = initComplete(),
                                      displayLength = 20,
                                      deferRender = TRUE,
                                      bLengthChange = FALSE,
                                      scrollX = 400,
                                      scrollY = 600,
                                      scroller = TRUE,
                                      ordering=FALSE,
                                      server = TRUE)
      )
      
      dt
    }
})



# output$chooseGOtoSave <- renderUI({
#     rv$widgets$go$groupGO_data
#     rv$widgets$go$enrichGO_data
#     if(is.null(rv$widgets$go$enrichGO_data) && is.null(rv$widgets$go$groupGO_data)){return(NULL)}
#     
#     .choices <- c()
#     if(!is.null(rv$widgets$go$groupGO_data)){.choices <- c(.choices, "Classification")}
#     if(!is.null(rv$widgets$go$enrichGO_data)){.choices <- c(.choices, "Enrichment")}
#     if(!is.null(rv$widgets$go$enrichGO_data) && !is.null(rv$widgets$go$groupGO_data)){.choices <- c(.choices, "Both")}
#     
#     radioButtons("whichGO2Save", "GO analysis to save", choices = .choices)
# })


## Validation of the GO analysis
# observeEvent(input$ValidGOAnalysis,ignoreInit =  TRUE,{ 
#     rv$widgets$go$Organism
#     rv$widgets$go$Ontology
#     rv$widgets$go$pvalueCutoff
#     req(rv$current.obj)
#     rv$widgets$go$enrichGO_data
#     rv$widgets$go$groupGO_data 
#     rv$widgets$go$universe
#     rv$widgets$go$whichGO2Save
#     
#     
#     if ((rv$widgets$go$ValidGOAnalysis == 0) ||  is.null(rv$widgets$go$ValidGOAnalysis) ) {
#         return()}
#     
#     isolate({
#         
#         result = tryCatch(
#             {
#                 
#                 
#                 textGOParams <- paste("Dataset of ",
#                                       rv$typeOfDataset,"GO analysis with ",
#                                       "organism = ", rv$widgets$go$Organism,
#                                       "ontology = ", rv$widgets$go$Ontology, sep= " ")
#                 
#                 
#                 switch(rv$widgets$go$whichGO2Save,
#                        Both =
#                        {temp <- GOAnalysisSave(rv$dataset[[rv$widgets$go$datasets]],
#                                                ggo_res = rv$widgets$go$groupGO_data ,
#                                                ego_res = rv$widgets$go$enrichGO_data ,
#                                                organism = rv$widgets$go$Organism,
#                                                ontology = rv$widgets$go$Ontology,
#                                                level = rv$widgets$go$GO_level,
#                                                pvalueCutoff = rv$widgets$go$pvalueCutoff,
#                                                typeUniverse = rv$widgets$go$universe)},
#                        Classification = 
#                        {temp <- GOAnalysisSave(rv$dataset[[rv$widgets$go$datasets]],
#                                                ggo_res = rv$widgets$go$groupGO_data ,
#                                                organism = rv$widgets$go$Organism,
#                                                ontology = rv$widgets$go$Ontology,
#                                                level = rv$widgets$go$GO_level)},
#                        
#                        Enrichment = 
#                        {temp <- GOAnalysisSave(rv$dataset[[rv$widgets$go$datasets]],
#                                                ego_res = rv$widgets$go$enrichGO_data ,
#                                                organism = rv$widgets$go$Organism,
#                                                ontology = rv$widgets$go$Ontology,
#                                                pvalueCutoff = rv$widgets$go$pvalueCutoff,
#                                                typeUniverse = rv$widgets$go$universe)}
#                        
#                 )
#                 
#                 #name <- paste("GOAnalysis - ", rv$typeOfDataset, sep="")
#                 #rv$dataset[[name]] <- temp
#                 #rv$current.obj <- temp
#                 
#                 
#                 #updateSelectInput(session, "datasets", 
#                 #                 # paste("Dataset versions of", rv$current.obj.name, sep=" "),
#                 #                  choices = names(rv$dataset),
#                 #                  selected = name)
#                 #updateRadioButtons(session, "whichGO2Save",selected = rv$widgets$go$whichGO2Save)
#                 
#                 # 
#                 # ####write command Log file
#                 # writeToCommandLogFile(paste("cond1 <- '", rv$widgets$go$condition1, "'", sep=""))
#                 # writeToCommandLogFile(paste("cond2 <- '", rv$widgets$go$condition2, "'", sep=""))
#                 # writeToCommandLogFile(paste("method <- '", rv$widgets$go$diffAnaMethod, "'", sep=""))
#                 # if (rv$widgets$go$diffAnaMethod == "Limma"){
#                 #     writeToCommandLogFile("data <- wrapper.diffAnaLimma(current.obj, cond1, cond2)")
#                 # } else if (rv$widgets$go$diffAnaMethod == "Welch"){
#                 #     writeToCommandLogFile( "data <- wrapper.diffAnaWelch(current.obj, cond1, cond2)")
#                 # }
#                 # 
#                 # 
#                 # writeToCommandLogFile(paste("threshold_pValue <- ", rv$widgets$go$seuilPVal, sep=""))
#                 # writeToCommandLogFile(paste("threshold_logFC <- ", rv$widgets$go$seuilLogFC,sep=""))
#                 # 
#                 # writeToCommandLogFile(paste("calibMethod <- \"", rv$widgets$go$calibrationMethod, "\"", sep=""))
#                 # if (rv$widgets$go$calibrationMethod == "Benjamini-Hochberg") { 
#                 #     writeToCommandLogFile("m <- 1") }
#                 # else if (rv$widgets$go$calibrationMethod == "numeric value") 
#                 # { writeToCommandLogFile(paste(" m <- ",as.numeric(rv$widgets$go$numericValCalibration), sep=""))}
#                 # else {writeToCommandLogFile("m <- calibMethod")}
#                 # 
#                 # writeToCommandLogFile("fdr <- diffAnaComputeFDR(data, threshold_pValue, threshold_logFC, m)")
#                 # 
#                 # 
#                 # writeToCommandLogFile(paste(" temp <- diffAnaSave(dataset[['",
#                 #                             rv$widgets$go$datasets,"']],  data, method, cond1, cond2, threshold_pValue, threshold_logFC, fdr, calibMethod)", sep=""))
#                 # writeToCommandLogFile(paste(" name <- \"DiffAnalysis.", 
#                 #                             rv$widgets$go$diffAnaMethod, ".", rv$typeOfDataset,"\"", sep="" ))
#                 # writeToCommandLogFile("dataset[[name]] <- temp")
#                 # writeToCommandLogFile("current.obj <- temp")
#                 # 
#                 # 
#                 # 
#                 # cMethod <- NULL
#                 # if (rv$widgets$go$calibrationMethod == "numeric value"){
#                 #     cMethod <- paste("The proportion of true null
#                 #                      hypotheses was set to", 
#                 #                      rv$widgets$go$numericValCalibration, sep= " ")}
#                 # else {cMethod <-rv$widgets$go$calibrationMethod }
#                 # 
#                 
#                 text2Log <- NULL
#                 
#                 switch(rv$widgets$go$whichGO2Save,
#                        Both =
#                        {
#                            
#                            text2Log <- paste(
#                                "ProtIDList <- Biobase::fData(current.obj)[,\"",rv$widgets$go$UniprotIDCol,"]\"\n",
#                                "levelIndex <- sort(",rv$widgets$go$GO_level,") \n",
#                                
#                                "index <- NULL\n",
#                                "if (\"Significant.Welch\" %in% names(Biobase::fData(current.obj) )){\n",
#                                "index <- which(Biobase::fData(current.obj)$Significant.Welch == TRUE)\n",
#                                "} else if (\"Significant.limma\" %in% names(Biobase::fData(current.obj) )){",
#                                "index <- which(Biobase::fData(current.obj)$Significant.limma == TRUE)\n",
#                                "} else{ index <- seq(1:nrow(current.obj))}\n",
#                                "groupGO_data <- list()\n",
#                                "for (i in 1:length(levelIndex)){\n",
#                                "groupGO_data[[i]] <- list(level = as.numeric(levelIndex[i]),\n",
#                                "ggo_res = group_GO(ProtIDList[index],\n",
#                                "\"",rv$widgets$go$idFrom,"\", 
#                                \"ENTREZID\", \n",
#                                "orgdb = \"",rv$widgets$go$Organism,"\",\n", 
#                                "ont=",rv$widgets$go$Ontology,",\n", 
#                                "level=as.numeric(levelIndex[i]))) }\n",
#                                # index <- GetDataIndexForAnalysis()
#                                # rv$enrichGO_data <- enrich_GO(rv$ProtIDList[index],
#                                #                               idFrom = rv$widgets$go$idFrom, 
#                                #                               idTo = "ENTREZID", 
#                                #                               orgdb = rv$widgets$go$Organism, 
#                                #                               ont = rv$widgets$go$Ontology, 
#                                #                               #pAdj = rv$widgets$go$PAdjustMethod, 
#                                #                               pval = rv$widgets$go$pvalueCutoff, 
#                                #                               universe = rv$universeData )
#                                # 
#                                
#                                
#                                "temp <- GOAnalysisSave(dataset[[datasets]],ggo_res = groupGO_data ,
#                                ego_res = enrichGO_data ,
#                                organism = \"",rv$widgets$go$Organism,"\",ontology = \"", rv$widgets$go$Ontology,"\",\n",
#                                "level = ", rv$widgets$go$GO_level,", pvalueCutoff = ", rv$widgets$go$pvalueCutoff,",\n",
#                                "typeUniverse = \"", rv$widgets$go$universe,"\")\n",
#                                " name <- \"GOAnalysis", ".", rv$typeOfDataset,"\"",
#                                "dataset[[name]] <- temp\n",
#                                "current.obj <- temp\n", sep= " ")
#                            # writeToCommandLogFile(text2Log)
#                        }
#                 )
#                 
#                # updateTabsetPanel(session, "tabsetPanel_GO", selected = "tabPanelSaveGO")
#                 
#                 
#                 
#             }
#             #, warning = function(w) {
#             #    shinyjs::info(conditionMessage(w))
#             #}
#             , error = function(e) {
#                 shinyjs::info(paste("Valid GO Analysis",":",
#                                     conditionMessage(e), sep=" "))
#             }, finally = {
#                 #cleanup-code 
#             })
#         
#         
#         
#     }) 
#     
# })




output$GO_resumeParams <- DT::renderDataTable(server=TRUE,{
  req(c(rv$widgets$go$sourceOfProtID,
        rv$widgets$go$idFrom,
        rv$widgets$go$Organism,
        rv$widgets$go$Ontology))
  
  if (length(rv$widgets$go$sourceOfProtID)==0){return(NULL)}
  
  
  rvModProcess$moduleGODone[4] <- TRUE
  
  l.params <- data.frame(param="sourceOfProtID", value=rv$widgets$go$sourceOfProtID)
  l.params <- rbind(l.params,data.frame(param="idFrom", value=as.character(rv$widgets$go$idFrom)))
  l.params <- rbind(l.params,data.frame(param="Organism", value=rv$widgets$go$Organism))
  l.params <- rbind(l.params,data.frame(param="Ontology", value=rv$widgets$go$Ontology))
  
  DT::datatable(l.params,
                escape = FALSE,
                rownames=FALSE,
                extensions = c('Scroller', 'Buttons'),
                options = list(initComplete = initComplete(),
                               buttons = list('copy',
                                              list(
                                                extend = 'csv',
                                                filename = 'GO_paramsUsed'
                                              ),'print'),
                               dom='Brt',
                               buttons = c('copy','excel', 'pdf', 'print'),
                               columnDefs = list(list(width='200px',targets= "_all")),
                               ordering = FALSE)
  )
  #}
})