inst/shiny/server/server_demultiplex.R

In wevanjohnson/animalcules.preprocess: This package contains tools and functions for preprocessing microbiome data

  #Barcode File Display  
  
  #Inputting data
  reactbarcode <- reactive ({
    req(input$barcode)
    barcodeFile <- read.table(input$barcode$datapath, header = input$headerbarcode, sep = "\t")
    barcodeFile 
  })
  #Updates slider
  observe({ 
    updateSliderInput (session,"displaybarcode",min=1,value=10,max=nrow(reactbarcode()))
  })
  #Display Index Data
  updatedisplaybarcode<- reactive({
    displayb<-reactbarcode()[1:input$displaybarcode,]
    return(displayb)
  })
  #Output Data
  output$tablebarcode <- renderDataTable({
    updatedisplaybarcode()[1:input$displaybarcode,]
  })
  
  #Update Hamming Distance Maximum
  observe({
    updateSelectInput(session,"hammingDist",choices=c(1:nchar(as.character(reactbarcode()[1,2]))),selected = 1)
  })
  
  #Index and Read File Display  
  
  #Inputting Index data
  reactindex <- reactive ({
    req(input$index)
    indexFile <- Biostrings::readDNAStringSet(input$index$datapath, format = "fastq", n=100)
    indexFile
  })
  
  #Inputting Read data
  reactread <- reactive ({
    req(input$read)
    readFile<- Biostrings::readQualityScaledDNAStringSet(input$read$datapath, n=100)
    readFile
  })
  
  #Updates slider
  observe({ 
    updateSliderInput (session,"display",min=1,value=10,max=100)
  })
  observeEvent(input$upload, {
    
    #Display Data
    updatedisplay<- reactive({
      Index<-reactindex()[1:input$display,]
      Read<-reactread()[1:input$display,]
      x<-cbind.data.frame(Index,Read)
      return(x)
    })
    #Output Data
    output$table <- renderTable({
      updatedisplay()[1:input$display,]
    })})
  
  
  #rcBarcodes
  
  rc<-reactive({
    return(as.logical(input$rcBarcodes))
  })  
  
  #hammingDist
  
  ham<-reactive({
    return(as.numeric(input$hammingDist))
  })
  
  
  out<-reactive({
    return(as.character(input$location))
  })  
  
  #Demultiplex
  observeEvent(input$demultiplex, {
    
    demultiplex(barcodeFile=input$barcode$datapath ,indexFile=input$index$datapath ,readFile = input$read$datapath,location=file.path(out(),"/Demultiplexed Sample Files"), rcBarcodes = rc(), cores= cores(), hammingDist= ham()) 
    
  })