server.R

if (!require("Rcpp")){
  install.packages("Rcpp")
}

if(!require(shinydashboard)){
  install.packages('shinydashboard')
  library(shinydashboard)
}

if(!require(rjson)){
  install.packages('rjson')
}

if(!require(devtools)){
  install.packages('devtools')
}

#library(plotly)

if (!require(psych)) {
  install.packages('psych')
  library(psych)
}

if (!require(ggplot2)) {
  install.packages('ggplot2')
  library(ggplot2)
}

if (!require(vegan)) {
  install.packages('vegan')
  library(vegan)
}

if (!require(dendextend)) {
  install.packages('dendextend')
  library(dendextend)
}

if (!require(circlize)) {
  install.packages('circlize')
  library(circlize)
}

if (!require(d3heatmap)) {
  install.packages('d3heatmap')
  library(d3heatmap)
}

if (!require(biom)) {
  install.packages('biom')
  library(biom)
}

if (!require(devtools)) {
  install.packages('devtools')
  library(devtools)
}

if (!require(scatterD3)) {
  install.packages('scatterD3')
  library(scatterD3)
}

if (!require(rNVD3)) {
  library(devtools)
  install_github('rNVD3', 'ramnathv')
  library(rNVD3)
}

if (!require(genefilter)) {
  source("https://bioconductor.org/biocLite.R")
  biocLite("genefilter")
  library(genefilter)
}

if (!require(googleVis)) {
  install.packages('googleVis')
  library(googleVis)
}

library(shinyjs)

# Allow to upload 50M files
options(shiny.maxRequestSize=50*1024^2) 
source("internal.R")

renderDataTable <- DT::renderDataTable
dataTableOutput <- DT::dataTableOutput

shinyServer(function(input, output,session) {
  
  
#####################################################
##
##                    LOAD FILES
##
#####################################################
  
  ## Create base for contrast
  rand = floor(runif(1,0,1e9))
  namesfile = tempfile(pattern = "BaseContrast", tmpdir = tempdir(), fileext = "")
  file.create(namesfile,showWarnings=FALSE)

  ## Popup messages
  observe(if(input$AddRegScatter) info("By adding the regression line, you will lose interactivity."))

  ## Counts file
  dataInputCounts <-reactive({ 
    
    inFile <- input$fileCounts
  
    if (is.null(inFile)) return(NULL)

    data = read.csv(inFile$datapath,sep="\t",header=TRUE)

    ## Rownames
    if(!TRUE%in%duplicated(data[,1])) rownames(data)=data[,1];data=data[,-1]

    return(as.data.frame(data))
  })
  


  ## Taxo File
  dataInputTaxo <-reactive({ 
    
    inFile <- input$fileTaxo
    
    if (is.null(inFile)) return(NULL)
    
    if(input$TypeTaxo=="Table") 
    {
      data = read.csv(inFile$datapath,sep="\t",header=TRUE)
      
      ## Rownames
      if(!TRUE%in%duplicated(data[,1])){ 
        DataNames=data[,1]
        colNames=colnames(data)[-1]
        data=as.matrix(data[,-1])
        rownames(data)=DataNames
        colnames(data) = colNames
        }
    }
    
    if(input$TypeTaxo=="RDP") 
    {
      data = read_rdp(inFile$datapath,input$RDP_th)
    }
    
    ## Add NA
    data=as.matrix(data)
    indNa = which(data=="")
    data[indNa]=NA
    
    return(as.data.frame(data))
  })


  ## BIOM File
  dataInputBiom <-reactive({ 
    
    inFile <- input$fileBiom
    
    if (is.null(inFile)) return(NULL)
    data = read_biom(inFile$datapath)
    
    return(data)
  })



  ## Input data
  dataInput <-reactive({ 
    
    data = NULL
    check = NULL
    percent = NULL
    
    if(input$FileFormat=="fileCounts")
    {
      Counts = dataInputCounts()
      Taxo = dataInputTaxo()
      if(!is.null(Counts) && !is.null(Taxo))
      { 
        tmp = GetDataFromCT(Counts,Taxo)
        data = list(counts=tmp$counts,taxo=tmp$taxo)
        check = list(CheckCounts=tmp$CheckCounts,CheckTaxo=tmp$CheckTaxo,CheckPercent=tmp$CheckPercent)
        percent = tmp$Percent
      }    
    }
    
    if(input$FileFormat=="fileBiom")
    {
      tmpBIOM = dataInputBiom()
      if(!is.null(tmpBIOM))
      {
        tmp = GetDataFromBIOM(tmpBIOM)
        data = list(counts=tmp$counts,taxo=tmp$taxo)
        check = list(CheckCounts=tmp$CheckCounts,CheckTaxo=tmp$CheckTaxo,CheckPercent=tmp$CheckPercent)
        percent = tmp$Percent
      }
    }
    
    return(list(data=data,check=check,percent=percent))
  })
  
  

  ## Merge counts data
  dataMergeCounts <-reactive({ 
    input$RunDESeq
    
    counts = NULL
    CheckTarget = FALSE
    normFactors = NULL
    CT_noNorm = NULL
    #labeled= NULL
    data = dataInput()$data
    target = isolate(dataInputTarget()$target)
    taxo = isolate(input$TaxoSelect)
    
    if(!is.null(data$counts) && !is.null(data$taxo) && nrow(data$counts)>0 && nrow(data$taxo)>0 && !is.null(taxo) && taxo!="..." && !is.null(target)) 
    {
      design = GetDesign(input)
      tmp = isolate(GetCountsMerge(input,data,taxo,target,design))
      counts = tmp$counts
      CheckTarget = tmp$CheckTarget
      #target = tmp$target
      #labeled = tmp$labeled
      normFactors = tmp$normFactors
      CT_noNorm = tmp$CT_noNorm
    }
    return(list(counts=counts,CheckTarget=CheckTarget,normFactors=normFactors,CT_noNorm=CT_noNorm))
    #return(list(counts=counts,target=target,labeled=labeled,normFactors=normFactors,CT_noNorm=CT_noNorm))
  })


  # Infobox Error counts
  output$InfoErrorCounts <- renderInfoBox({
    
    tmp = dataInput()
    data = tmp$data
    check = tmp$check
    cond = (!is.null(data$counts) && nrow(data$counts)>0)
    res =infoBox(h6(strong("Count table")), subtitle = h6("Load the count table") ,color = "light-blue",width=NULL,fill=TRUE, icon = icon("upload"))
    
    if(cond)
    {
      if(!is.null(check$CheckCounts$Warning)) res = infoBox(h6(strong("Count table")), subtitle = h6(check$CheckCounts$Warning), icon = icon("warning"),color = "orange",width=NULL,fill=TRUE)
      if(!is.null(check$CheckCounts$Error)) res = infoBox(h6(strong("Count table")), subtitle = h6(check$CheckCounts$Error), icon = icon("thumbs-o-down"),color = "red",width=NULL,fill=TRUE)
      if(is.null(check$CheckCounts$Error) && is.null(check$CheckCounts$Warning)) res = infoBox(h6(strong("Count table")), subtitle = h6(paste("Format of the count table seems to be OK")), icon = icon("thumbs-o-up"),color = "green",width=NULL,fill=TRUE)
    }
    
    return(res)
  })

  # Infobox Error counts
  output$InfoErrorTaxo <- renderInfoBox({
    
    tmp = dataInput()
    data = tmp$data
    check = tmp$check
    cond = (!is.null(data$taxo) && nrow(data$taxo)>0)
    res =infoBox(h6(strong("Taxonomy table")), subtitle = h6("Load the taxonomy table") ,color = "light-blue",width=NULL,fill=TRUE, icon = icon("upload"))
    
    if(cond)
    {
      if(!is.null(check$CheckTaxo$Warning)) res = infoBox(h6(strong("Taxonomy table")), subtitle = h6(check$CheckTaxo$Warning), icon = icon("warning"),color = "orange",width=NULL,fill=TRUE)
      if(!is.null(check$CheckTaxo$Error)) res = infoBox(h6(strong("Taxonomy table")), subtitle = h6(check$CheckTaxo$Error), icon = icon("thumbs-o-down"),color = "red",width=NULL,fill=TRUE)
      if(is.null(check$CheckTaxo$Error) && is.null(check$CheckTaxo$Warning)) res = infoBox(h6(strong("Taxonomy table")), subtitle = h6(paste("Format of the taxonomy table seems to be OK")), icon = icon("thumbs-o-up"),color = "green",width=NULL,fill=TRUE)
    }
    
    return(res)
  })


  # Infobox Error counts
  output$valueErrorPercent <- renderInfoBox({
    
    tmp = dataInput()
    data = tmp$data
    check = tmp$check
    cond = (!is.null(data$counts) && nrow(data$counts)>0 && !is.null(data$taxo) && nrow(data$taxo)>0)
    res = valueBox(paste0(0, "%"),h6(strong("Annotated features")), color = "light-blue",width=NULL,icon = icon("list"))
    
    if(cond)
    {
      percent = round(100*tmp$percent,2)
      if(percent==0) res = valueBox(paste0(percent, "%"),h6(strong("Annotated features")), color = "red",width=NULL,icon = icon("list"))  
      if(percent!=0) res = valueBox(paste0(percent, "%"),h6(strong("Annotated features")), color = "green",width=NULL,icon = icon("list"))  
      
    }
    
    return(res)
  })


  
#####################################################
##
##                DYNAMIC MENU
##
#####################################################
  
  
  
  output$dymMenu <- renderMenu({
    
    tmp = dataInput()
    data = tmp$data
    check = tmp$check
    
    ## Check error in the counts and taxonomy table 
    CheckOK = (is.null(check$CheckCounts$Error) && is.null(check$CheckTaxo$Error)  && is.null(check$CheckPercent))

    if(!is.null(data$counts) && !is.null(data$taxo) && nrow(data$counts)>0 && nrow(data$taxo)>0 && CheckOK)
    {
      sidebarMenu(
        menuItem("Statistical analysis",
                 menuSubItem("Run differential analysis",tabName="RunDiff"),
                 menuSubItem("Diagnostic plots",tabName="DiagPlotTab"),
                 menuSubItem("Tables",tabName="TableDiff"),
                 icon = icon("bar-chart-o"), tabName = "AnaStat"
        ),
        menuItem("Visualization",icon = icon("area-chart"), tabName = "Visu"),
        menuItem("Perspective plots", icon = icon("pie-chart"), tabName = "Krona")

      )
     }
    else{
      sidebarMenu()
    }
    
  })
  
  

  #####################################################
  ##
  ##                DATA TABLE
  ##
  #####################################################
  
  ## Counts Table
  output$DataCounts <- renderDataTable(
    dataInput()$data$counts, 
    options = list(lengthMenu = list(c(10, 50, -1), c('10', '50', 'All')),
                   pageLength = 10,scrollX=TRUE
    ))
  
  ## Taxonomy table
  output$DataTaxo <- renderDataTable(
    dataInput()$data$taxo, 
    options = list(lengthMenu = list(c(10, 50, -1), c('10', '50', 'All')),
                   pageLength = 10,scrollX=TRUE
    ))

  
  ## Tab box for data visualisation
  output$TabBoxData <- renderUI({
    
    data=dataInput()$data
    
    if(!is.null(data$counts) && !is.null(data$taxo) && nrow(data$counts)>0 && nrow(data$taxo)>0)
    {
      tabBox(width = NULL, selected = "Count table",
             tabPanel("Count table",dataTableOutput("DataCounts")),
             tabPanel("Taxonomy",dataTableOutput("DataTaxo")),
             tabPanel("Summary",h5(strong("Percentage of annotation")),htmlOutput("SummaryView"),
                      br(),h5(strong("Number of features by level:")),plotOutput("SummaryViewBarplot",width = 1200,height=500))
      )
    }
    
  })

  output$SummaryView <- renderGvis({
    data = dataInput()$data
    taxo = data$taxo
    counts = data$counts
    res = NULL
    if(!is.null(data$counts) && !is.null(data$taxo) && nrow(data$counts)>0 && nrow(data$taxo)>0)
    {
      taxo = rbind(taxo,rep(NA,ncol(taxo)))
      tmpPercent = round(apply(is.na(taxo),2,table)["FALSE",]/nrow(counts)*100,2)

      #print(tmpPercent)
      df <- data.frame(Label = colnames(taxo),Value = tmpPercent)
    
      res = gvisGauge(df,options=list(min=0, max=100, greenFrom=80,
                                    greenTo=100, yellowFrom=60, yellowTo=80,
                                    redFrom=0, redTo=60, width=1200, height=300))
    }
    return(res)
  })
  
  
  output$SummaryViewBarplot <- renderPlot({
    data = dataInput()$data
    taxo = data$taxo
    counts = data$counts
    res = NULL
    if(!is.null(data$counts) && !is.null(data$taxo) && nrow(data$counts)>0 && nrow(data$taxo)>0)
    {
      colors=rep(c("#1f77b4","#aec7e8","#ff7f0e","#ffbb78", "#2ca02c","#98df8a","#d62728","#ff9896","#9467bd","#c5b0d5","#8c564b",
                   "#c49c94","#e377c2","#f7b6d2","#7f7f7f", "#c7c7c7","#bcbd22","#dbdb8d","#17becf","#9edae5"),ceiling(ncol(taxo)/20))
      tmp = apply(taxo,2,unique)
      nbfeatures = as.numeric(lapply(tmp,length)) -as.numeric(lapply(lapply(tmp,is.na),any))
      df <- data.frame(Label = colnames(taxo),Count = nbfeatures)
      df$Label = factor(df$Label,levels =colnames(taxo) )
      res = ggplot(df,aes(x=Label,y=Count,fill=Label))+geom_bar(stat="identity")
      res = res + theme_bw() + xlab("Taxonomy") + scale_fill_manual(values=colors) + guides(fill=FALSE)
    }
    return(res)
  })
  
  #####################################################
  ##
  ##                TARGET FILE
  ##
  #####################################################
  

  ## Load target file
  dataInputTarget <-reactive({ 
    
    inFile <- input$fileTarget
    counts = dataInput()$data$counts
    
    
    if (is.null(inFile)) return(NULL)
    
    
    data = read.csv(inFile$datapath,sep="\t",header=TRUE)
    rownames(data) <- as.character(data[, 1])
    ind = which(rownames(data)%in%colnames(counts))
    #ord = order(rownames(data))
    #data = data[ord,]
    ### A SUPPRIMER 
    #rownames(data) <- colnames(counts)
    
    # Percent annotated
#     print(ind)
#     print(colnames(counts))
#     print(rownames(data))
    labeled = length(ind)/length(colnames(counts))*100.0
    
    return(list(target=data[ind,], labeled=labeled))
  })



  ## Interest Variables
  output$SelectInterestVar <- renderUI({
        
    target=dataInputTarget()$target
    
    if(!is.null(target)) 
    {
      namesTarget = colnames(target)[2:ncol(target)]
      selectInput("InterestVar",h6(strong("Select the variables")),namesTarget,selected=namesTarget,multiple=TRUE)
    }
  
  })


  ## Interactions
  output$SelectInteraction2 <- renderUI({
        
    target = dataInputTarget()$target

    if(!is.null(target)) 
    {
      Interac = GetInteraction2(target)
      selectInput("Interaction2",h6(strong("Add interactions")),Interac,selected=NULL,multiple=TRUE)
    }
    
  })


  ## Reference radio buttons
  output$RefSelect <- renderUI({
    
    target = dataInputTarget()$target
    RB=list()
    if(!is.null(target)) 
    {
      InterVar = input$InterestVar
      if(length(InterVar)>0)
      {
        names = paste0("Ref",InterVar)
          for(i in 1:length(names))
          {
            val = unique(target[,InterVar[i]])
            RB[[i]] = selectInput(names[i],paste("Reference for",InterVar[i]),as.vector(val))
          }
      }
    }
    return(RB)
    
  })


  # Infobox design
  output$RowTarget <- renderInfoBox({
    #target = dataInputTarget()
    #labeled = dataMergeCounts()$labeled
    labeled = dataInputTarget()$labeled
    if(!is.null(labeled)) 
    {
      #### Ajout fontion check target
      #infoBox(h6(strong("Target file")), subtitle = h6("Your target file is OK"), icon = icon("thumbs-o-up"),color = "green",width=NULL,fill=TRUE)
      labeled = round(labeled,2)
      if(labeled>0) res = valueBox(paste0(labeled, "%"),h6(strong("Labeled features")), color = "green",width=NULL,icon = icon("list"))
      else res = valueBox(paste0(labeled, "%"),h6(strong("Labeled features")), color = "red",width=NULL,icon = icon("list"))  
    }
    #else infoBox(h6(strong("Target file")), subtitle = h6("Label of the target file must correspond to count table column names") ,color = "light-blue",width=NULL,fill=TRUE, icon = icon("warning"))
    else res = valueBox(paste0(0, "%"),h6(strong("Labeled features")), color = "light-blue",width=NULL,icon = icon("list"))
    return(res)
  }
  )




  ## target table
  output$DataTarget <- renderDataTable(
  dataInputTarget()$target,
  options = list(lengthMenu = list(c(10, 50, -1), c('10', '50', 'All')),
                 pageLength = 10,scrollX=TRUE
  ))

  ## Counts table for the selected taxonomy level
  output$CountsMerge <- renderDataTable(
    round(counts(ResDiffAnal()$dds,normalized=TRUE)),
    options = list(lengthMenu = list(c(10, 50, -1), c('10', '50', 'All')),
                   pageLength = 10,scrollX=TRUE
    ))


  ## Box for merged counts
  output$BoxCountsMerge <- renderUI({
    
    counts = dataMergeCounts()$counts
    taxo = input$TaxoSelect
    
    if(!is.null(counts) && taxo != "...")
    {
      box(title=paste("Count table (",taxo,")",sep=""),width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed = TRUE,
          dataTableOutput("CountsMerge"),
          downloadButton('ExportCounts', 'Export normalised counts'),
          downloadButton('ExportRelative', 'Export relative abundance')
      )  
    }
    
  })

  ## Export in .csv
  output$ExportCounts <- downloadHandler(
    filename = function() { 'NormCounts.csv' },
    content = function(file){write.csv(dataMergeCounts()$counts, file)}
  )

  ## Export in .csv
  output$ExportRelative <- downloadHandler(
    filename = function() { 'RelativeAb.csv' },
    content = function(file){write.csv(dataMergeCounts()$counts/colSums(dataMergeCounts()$counts), file)}
  )


  ## Box for target visualisation
  output$BoxTarget <- renderUI({
    
    target = dataInputTarget()$target

    if(!is.null(target) &&  nrow(target)>0)
    {
      box(title="Target file overview",width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed = TRUE,
          dataTableOutput("DataTarget")
      )  
    }
    
  })



#####################################################
##
##            DEFINE CONTRAST
##
#####################################################
  
  output$contrastMat <- renderUI({
    
    resDiff = ResDiffAnal()
    dds = resDiff$dds
    names = resultsNames(dds)

    Contrast=list()
    
    for(i in 1:length(names)){Contrast[[i]] = numericInput(names[i],names[i],0,step=1,min=-1,max=1)}
  
    return(Contrast)
    
  })


  output$ContrastOverview <- renderPrint({
    
    resDiff = ResDiffAnal()
    dds = resDiff$dds
    names = resultsNames(dds)
    
    cont = input$ContrastList
    filesize = file.info(namesfile)[,"size"]
    if(is.na(filesize)){filesize=0}
    if(filesize!=0)
    { 
      ContrastBase = read.table(namesfile,header=TRUE)
      ind = which(colnames(ContrastBase)%in%cont)
      div(HTML(PrintContrasts(names,sapply(ContrastBase[,ind],as.numeric),cont)))
    }
  })


  ## Add contrast function
  AddCont <-eventReactive(input$AddContrast,{
    
    resDiff = ResDiffAnal()
    dds = resDiff$dds
    names = resultsNames(dds)

    BaseContrast(input,names,namesfile)
    filesize = file.info(namesfile)[,"size"]
    if(is.na(filesize)){filesize=0}
    if(filesize!=0) tmp = read.table(namesfile,header=TRUE)
    Contrast = colnames(as.matrix(tmp))
    updateSelectInput(session, "ContrastList","Contrasts",Contrast)
    updateSelectInput(session, "ContrastList_table","Contrasts",Contrast)
    updateSelectInput(session, "ContrastList_table_Visu","For which contrasts",Contrast)
    updateSelectInput(session, "ContrastList_table_FC","Contrasts (Min = 2)",Contrast)
  })

  ## Add contrast 
  observeEvent(input$AddContrast,{  
    
    AddCont()
    
  },priority=1)


  ## Add contrast function
  AddContEasy <-eventReactive(input$AddContrastEasy,{
    
    resDiff = ResDiffAnal()
    dds = resDiff$dds
    names = resultsNames(dds)
#     
#     BaseContrast(input,names,namesfile)
#     tmp = read.table(namesfile,header=TRUE)
#     Contrast = colnames(as.matrix(tmp))
    updateSelectInput(session, "ContrastList","Contrasts",Contrast)
    updateSelectInput(session, "ContrastList_table","Contrasts",Contrast)
    updateSelectInput(session, "ContrastList_table_Visu","For which contrasts",Contrast)
    updateSelectInput(session, "ContrastList_table_FC","Contrasts (Min = 2)",Contrast)
  })
  
  ## Add contrast 
  observeEvent(input$AddContrastEasy,{  
    
    AddContEasy()
    
  })


  AddContFromFile <-eventReactive(input$fileContrast,{ 
    
    res = ReadContrastFile()
    createdCont = NULL
    filesize = file.info(namesfile)[,"size"]
    if(is.na(filesize)){filesize=0}
    if(filesize!=0){ createdCont = read.table(namesfile,header=TRUE) }
      
    if(!is.null(res))
    { 
      if(!is.null(createdCont)) res = cbind(res,createdCont)
      updateSelectInput(session, "ContrastList","Contrasts",colnames(res))
      updateSelectInput(session, "ContrastList_table","Contrasts",colnames(res))
      updateSelectInput(session, "ContrastList_table_Visu","For which contrasts",colnames(res))
      updateSelectInput(session, "ContrastList_table_FC","Contrasts (Min = 2)",colnames(res))
      write.table(res,namesfile,row.names=FALSE)
    }
  })
 
 observeEvent(input$fileContrast,{ 
    
   AddContFromFile()
  },priority=1)


  ## Remove contrast function
  RemoveCont <-eventReactive(input$RemoveContrast,{
    
    ## get the size of the contrast base file
    filesize = file.info(namesfile)[,"size"]
    if(is.na(filesize)){filesize=0}
    if(filesize!=0)
    { 
      tmp = read.table(namesfile,header=TRUE)
      ind = which(colnames(tmp)%in%input$ContrastList)
      matKept = as.matrix(tmp[,-ind])
      ContrastKept = colnames(tmp)[-ind]
      
      if(ncol(matKept)>0) write.table(matKept,namesfile,row.names=FALSE,col.names = ContrastKept)
      else file.create(namesfile,showWarnings=FALSE)
      updateSelectInput(session, "ContrastList","Contrasts",ContrastKept)
      updateSelectInput(session, "ContrastList_table","Contrasts",ContrastKept)
      updateSelectInput(session, "ContrastList_table_Visu","For which contrasts",ContrastKept)
      updateSelectInput(session, "ContrastList_table_FC","Contrasts (Min = 2)",ContrastKept)
    }
  })
  
  
  
  ## Remove contrast
  observeEvent(input$RemoveContrast,{  
    
    RemoveCont()
    
  },priority=1)

  ## Remove all contrasts
  RemoveAllCont <-eventReactive(input$RunDESeq,{
    
      file.create(namesfile,showWarnings=FALSE)
      updateSelectInput(session, "ContrastList","Contrasts",NULL)
      updateSelectInput(session, "ContrastList_table","Contrasts",NULL)
      updateSelectInput(session, "ContrastList_table_Visu","For which contrasts",NULL)
      updateSelectInput(session, "ContrastList_table_FC","Contrasts (Min = 2)",NULL)
  })

  ## Remove all contrast
  observeEvent(input$RunDESeq,{  
    
    RemoveAllCont()
    
  })

# Infobox Contrast
output$InfoContrast <- renderInfoBox({
  input$RunDESeq
  input$AddContrast
  input$RemoveContrast
  input$fileContrast
  resDiff = ResDiffAnal()
  res=NULL
  if(!is.null(resDiff)){
  
    res = infoBox("Contrasts", subtitle = h6("At least one contrast (non null) must be defined"), icon = icon("warning"),color = "light-blue",width=NULL,fill=TRUE)
    test = FALSE
    filesize = isolate(file.info(namesfile)[,"size"])
    
    if(is.na(filesize)){filesize=0}
    if(filesize!=0) 
    {
      tmp = read.table(namesfile,header=TRUE)
      if(any(as.vector(tmp)!=0)) test = TRUE
    }
    
    if(test) res = infoBox("Contrasts", subtitle = h6("Contrasts OK"), icon = icon("thumbs-o-up"),color = "green",width=NULL,fill=TRUE)
  }
    return(res)
  })


  
  output$contrastBox <- renderUI({
    
    resDiff = ResDiffAnal()
    int = input$Interaction2
    target = resDiff$target
    
    InterVar = input$InterestVar
    ModInterestAll = unique(target[,InterVar])
    test = c()
    for(i in 1:length(InterVar)){ test =c(test,input$Select1_contrast%in%target[,InterVar[i]]) }
    
    ModInterestCond = unique(target[,which(test)])
    #alltmp = c(InterVar,Interaction)
    
    if(!is.null(resDiff))
    { 
      box(title="Contrasts",width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed = FALSE,
          fluidRow(
            column(width=3,selectInput("Select1_contrast",label=h6(strong("Compare")),ModInterestAll)),
            column(width=3,selectInput("Select2_contrast",label=h6(strong("To")),ModInterestCond)),
            if(length(int)>=1) column(width=3,selectInput("Select3_contrast",label=h6(strong("For")),c("All","WT","Delta"))),
            column(width=3,br(),br(),actionButton("AddContrastEasy","Add",icon = icon("plus")))
          )
      )
    }
    
  })


  output$contrastBoxAdvanced <- renderUI({
    
    resDiff = ResDiffAnal()
    
    if(!is.null(resDiff))
    { 
      box(title="Contrasts (advanced user)",width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed = FALSE,
          fluidRow(
            column(width=12,
                   fileInput('fileContrast', h6(strong('Select a file of contrasts')),width="60%")
            ),
            hr(),
            column(width=12,h6(strong("Define contrasts by yourself"))),
            column(width=6,textInput("ContrastName",label = NULL,value = "Contrast name")),
            column(width=6,actionButton("AddContrast","Add contrast",icon = icon("plus")))
          ),
          fluidRow(column(width=12,uiOutput("contrastMat")))
      )
    }
    
  })


  output$contrastDefined <- renderUI({
    resDiff = ResDiffAnal()
    
    if(!is.null(resDiff))
    { 
      box(title="Defined contrasts",width = NULL, status = "primary", solidHeader = TRUE,collapsible = FALSE,collapsed = FALSE,
          fluidRow(
            column(width=11,
                   selectInput("ContrastList","Contrasts","",multiple=TRUE,size=4,selectize=FALSE,width = '100%'),
                   fluidRow(
                      column(width=6,actionButton("RemoveContrast","Remove",icon = icon("remove"))),
                      column(width=6,downloadButton("exportContrast", "Export"))
                   ),
                   htmlOutput("ContrastOverview")
            )
            
          )
      )
    }
  })


  ReadContrastFile <-reactive({ 
    
    inFile <- input$fileContrast
    
    if (is.null(inFile)) return(NULL)
    
    res = read.csv(inFile$datapath,sep=" ",header=TRUE)
    
    return(res)
  })
  

  output$exportContrast <- downloadHandler(
    filename <- function() {"Contrasts.txt"},
    content <- function(file) {
      file.copy(namesfile,file)
    }
  )




#####################################################
##
##                DESEQ2 run
##
#####################################################



  # Infobox Contrast
  output$InfoDESeq <- renderInfoBox({
      input$RunDESeq
      
      resDiff = ResDiffAnal()
      if(!is.null(resDiff)){
        infoBox(h6(strong("Statistical analysis")), subtitle = h6("Differential analysis is done !"), icon = icon("thumbs-o-up"),color = "green",width=NULL,fill=TRUE)
      }

    
  })
  

  ## Get the results from DESeq2
  ResDiffAnal <-eventReactive(input$RunDESeq,{
    
    counts = dataMergeCounts()$counts
    CT_noNorm = dataMergeCounts()$CT_noNorm
    normFactors = dataMergeCounts()$normFactors
    ## HEEEERRREE
    target = dataInputTarget()$target
    #print(target)
    design = GetDesign(input)
   
    Get_dds_object(input,counts,target,design,normFactors,CT_noNorm)

    
  })


  ## Run DESeq2 via RunDESeq button
  observeEvent(input$RunDESeq,{
    withProgress(message="Analysis in progress...",ResDiffAnal())
  })

  
#####################################################
##
##                Taxonomy
##
#####################################################
  
  
  # Infobox Contrast
  output$SelectTaxo <- renderUI({
    
    data = dataInput()$data
    if(!is.null(data$taxo) && nrow(data$taxo)>0)
    { 
      tmp = colnames(data$taxo)
      selectInput("TaxoSelect",h6(strong("Select the taxonomy level")),c("...",tmp,"OTU"))
    }
    else selectInput("TaxoSelect",h6(strong("Select the taxonomy level")),c("..."))

  })
  


  
  # Infobox taxo
  output$InfoTaxo <- renderInfoBox({
  
    data = dataInput()$data
    taxo = input$TaxoSelect
    
    if(!is.null(data$counts) && !is.null(data$taxo) && nrow(data$counts)>0 && nrow(data$taxo)>0 && !is.null(taxo) && taxo!="...") 
    {
      counts = dataMergeCounts()$counts
      nfeature = nrow(counts)
      infoBox(h6(strong("Taxonomy")), subtitle = h6(paste(taxo, ", nb features: ",nfeature,sep="")), icon = icon("thumbs-o-up"),color = "green",width=NULL,fill=TRUE)
    }
    else infoBox(h6(strong("Taxonomy")), subtitle = h6("Select the taxonomy for the analysis") ,color = "light-blue",width=NULL,fill=TRUE, icon = icon("warning"))
  })



#####################################################
##
##                Diagnostic plots
##
#####################################################


  
  output$VarIntDiag <- renderUI({
    
    target=dataInputTarget()$target
    
    if(!is.null(target)) 
    {
      namesTarget = colnames(target)[2:ncol(target)]
      selectizeInput("VarInt",h6(strong("Select the variables of interest (max 2)")),namesTarget, selected = namesTarget[1],multiple = TRUE,options = list(maxItems = 2))
    }
    
  })
  
  
  output$PlotDiag <- renderPlot({
    input$RunDESeq
    
    resDiff = isolate(ResDiffAnal())
    Plot_diag(input,resDiff)
  },height = reactive(input$heightDiag))



  output$PlotpcoaEigen <- renderPlot({
    
    resDiff = ResDiffAnal()
    Plot_diag_pcoaEigen(input,resDiff)
  },height = 400)

  output$PlotEigen <- renderPlot({
    
    resDiff = ResDiffAnal()
    Plot_diag_Eigen(input,resDiff)
  },height =400)

  SizeFactor_table <-reactive({ 
    res = ResDiffAnal()