module1.R

#raw data tab
#tabPanel("Raw Data",

Module_Raw_data_UI<- function(id)
{
  ns<-NS(id)
  tagList(
    
    
    
    #Select organism
    fluidRow(column(2,
                    br(),
                    br(),
                    selectInput(ns("organism"), label = h5("Select organism"), 
                                choices = list("","Human" = 1, "Mouse" = 2),
                                selected = 1))),
    #select refrence genome
    fluidRow(column(2,
                    selectInput(ns("refgenome"), label = h5("Select reference genome"),
                                choices = list("", "BioMart" = 1, "Own upload" = 2),
                                selected = NULL)),
             column(1,
                    br(),
                    br(),
                    actionButton(ns("help1"), "Help"))),
    
    uiOutput(ns("inp_ch")),
    
    fluidRow(column(4,uiOutput(ns("file_ref_genome")))),
    
    fluidRow(column(4,uiOutput(ns("file3")))),

    #Read expression table
    fluidRow(column(4,uiOutput(ns("file1")))),

    #Read annotation table
    # #conditionalPanel("input.file1",
    fluidRow(column(4,uiOutput(ns("file2")))),#,
    #
    bsModal(ns("modalhelp"), "Selection of a reference genome", ns("help1"),  
            helpText('When using Kallisto Data, a gene annotation file is needed, which
                     links transcript identifiers to gene names.\n
                     Either select the BioMart Database to construct a gene annotation file 
                     or upload your own file.\n
                     In case of uploading your own file, it must be a .csv or .tsv file 
                     containing a column called "TXNAME" which holds the ensembl transcript id versions 
                     and a column called "SYMBOL" containing the external gene names / gene symbols.'))
  )
}

  

Module_Raw_data_Input<-function(input,output,session)
{
  
  #Step 1: Raw data tab
  #Aim: Display count/expression table and annotation table
  #Procedure:
  #Option 1: Generate count table from kallisto file and upload annotation table
  #Take kallisto file path as input
  #Upload annotation table
  #Option 2: Upload Count/expression table and annotation table
  #Upload count table/expression table and annotation table from file
  #observeEvent(input$reset_button, {js$reset()})  
  
  #Function that reads data from a file
  # input$file1 will be NULL initially. After the user selects
  # and uploads a file, it will be a data frame with 'name',
  # 'size', 'type', and 'datapath' columns. The 'datapath'
  # column will contain the local filenames where the data can
  # be found.
  print("module 1 line 56 ok")
  input_file <- function(in_file)
  {
    if(is.null(in_file))
    {
      return (NULL)
    }
    else
      return(read.csv(in_file$datapath, header = TRUE,sep = "\t",check.names = FALSE,quote = "\"")) 
  }
  
  output$inp_ch<-renderUI({
    if(input$organism!="")
      radioButtons(session$ns("filechoice"), "Choose starting point", 
                   choices = list("kallisto"=1, "count table"=2),selected = 2 )
  })
   
  #Option 1:  start with kallisto
  #Input kallisto file path to compute count table/expression table to be displayed
   output$file3<-renderUI({
                    
                    # validate(need(try(input$organism!=""),"Please choose organism under study"))
                    #validate(need(try(as.numeric(input$filechoice)!=0),"Please choose input source"))
                    # print(as.numeric(input$filechoice))
                    req(input$filechoice)
                    if(as.numeric(input$filechoice)==1 && input$organism!="")
                    {
                      #shinyDirButton("dir", "Chose directory","Upload")
                      textInput(session$ns("kallisto_path"), "Kallisto path", value = "")#E:/Zenitha/kallisto")
                    }
                  })
   
   output$file_ref_genome <- renderUI({
     if(as.numeric(input$refgenome == 2)){
       fileInput(session$ns("refgenome_path"), label = h5('Choose Reference genome file to upload'),
                 accept = c(
                   'text/csv',
                   'text/comma-separated-values',
                   'text/tab-separated-values',
                   'text/plain',
                   '.csv',
                   '.tsv'
                 ))
     }
      # textInput(session$ns("refgenome_path"), "Reference genome path", value = "")
   })
   
   
  
  #compute expression table/count table
  #t2g--->txi
  #This reactive prepeares input for the reactive txi which generates count table from kallisto files
   t2g<-reactive({
     if (!exists("mart")) {
       org<-NULL
       if(as.numeric(input$organism==1)) org<-"hsapiens_gene_ensembl"
       else if(as.numeric(input$organism==2)) org<-"mmusculus_gene_ensembl"
       mart <-
         biomaRt::useMart(
           #host = "jul2017.archive.ensembl.org",
           #host = "uswest.ensembl.org",
           #host="grch37.ensembl.org",#,
           host="ensembl.org",#
           #host="useast.ensembl.org",
           biomart = "ENSEMBL_MART_ENSEMBL",
           dataset = org)
       print(mart)
       t2g <- biomaRt::getBM(
         attributes = c("ensembl_transcript_id_version",
                        "ensembl_gene_id",
                        "external_gene_name"),
         mart = mart
       )
       print(head(t2g))
       t2g
     }
   })
  # create the count matrix out of the kallisto abundance table
  txi <-
    reactive( {
      #validate(need(try(input$kallisto_path!=""),"Please enter path of kallisto file"))
      if (as.numeric(input$filechoice)==1 && input$kallisto_path!=""){
        print("module 1 line 126 ok")
        # Create a Progress object
        progress <- shiny::Progress$new()
        # Make sure it closes when we exit this reactive, even if there's an error
        on.exit(progress$close())

        progress$set(message = "Processing kallisto files", value = 0)

        print(dir(input[["kallisto_path"]]))
        print(sapply(dir(input[["kallisto_path"]]),
                     function(id)
                     {
                       #file.path(input[["kallisto_path"]], id,"*.tsv")
                       print("143")
                       print(file.path(input[["kallisto_path"]],id, "*.h5"))
                       #list.files(
                         file.path(input[["kallisto_path"]],id, "*.h5")
                     }
                      
        ))
        
        # Increment the progress bar, and update the detail text.
        progress$inc(1/2, detail = paste("Doing part", 1,"/",2))
        # Pause for 0.1 seconds to simulate a long computation.
        Sys.sleep(0.1)
        
        if(as.numeric(input$refgenome==1))
        {
          d<-tximport(sapply(dir(input[["kallisto_path"]]),
                                           function(id)
                                           {
                                             print("154")
                                             print(list.files(file.path(input[["kallisto_path"]],id), "*.h5",full.names = T))
                                             list.files(
                                               file.path(input[["kallisto_path"]],id)
                                               , "*.h5"
                                               , full.names=TRUE)
                                           }
          ),#kallisto/abundance.h5
          "kallisto",
          tx2gene = t2g()[, c("ensembl_transcript_id_version",
                              "external_gene_name")]
          )
          print(head(t2g()))
          print("line 189")
          print(head(d))
        }
        else
        {
          #input_data<-input_file(input$refgenome_path)
          
          t2x <- read.delim(file=input$refgenome_path$datapath, sep=",")
          # t2x<-merge.data.frame(x = t2g(), y = t2x, 
          #                       by.x = "ensembl_transcript_id_version", by.y = "TXNAME")
          t2x<-t2x[,c("TXNAME", "SYMBOL")]
          d<-tximport(sapply(dir(input[["kallisto_path"]]),
                                           function(id)
                                           {
                                             print("154")
                                             print(list.files(file.path(input[["kallisto_path"]],id), "*.h5",full.names = T))
                                             list.files(
                                               file.path(input[["kallisto_path"]],id)
                                               , "*.h5"
                                               , full.names=TRUE)
                                           }
          ),#kallisto/abundance.h5
          "kallisto",
          tx2gene = t2x
          #geneIdCol = "external_gene_name",
          #txOut = T,
          #ignoreTxVersion = TRUE
          )
        }
        
        print("line 184")
        
        # Increment the progress bar, and update the detail text.
        progress$inc(2/2, detail = paste("Doing part", 2,"/",2))

        # Pause for 0.1 seconds to simulate a long computation.
        Sys.sleep(0.1)
        print("module 1 line 164")
        
        d
      }
    })

  #Option2: Upload count/expression table and annotation table from user

  #Input file containing count table/expression table as input from user
             output$file1<-renderUI({
                   
                   #validate(need(try(input$organism)!="","Please choose organism under study"))
               req(input$filechoice)
                   if(as.numeric(input$filechoice)==2)
                   {
                     fileInput(session$ns("file1"), label = h5('Choose Expression file to upload'),
                               accept = c(
                                 'text/csv',
                                 'text/comma-separated-values',
                                 'text/tab-separated-values',
                                 'text/plain',
                                 '.csv',
                                 '.tsv'
                               )
                     )
                   }
                   
                 })
                 #Input file containing annotation file as input from the user
                 output$file2<-renderUI({
                   # validate(need(try(input$organism!=""),"Please choose organism under study"),
                   #          need(try(!is.null(input$filechoice)),"Please choose startng point of input"))
                   # if( input$organism!="" && !is.null(input$filechoice))
                   # {
                   req(input$filechoice)
                   print("line 194 ok")
                   #print(as.numeric(input$filechoice))
                   
                   
                   if(as.numeric(input$filechoice)==2)#!is.null(input$file1) && 
                   {
                     req(input$file1)
                     fileInput(session$ns("file2"), label = h5('Choose Annotation file to upload'),
                               accept = c(
                                 'text/csv',
                                 'text/comma-separated-values',
                                 'text/tab-separated-values',
                                 'text/plain',
                                 '.csv',
                                 '.tsv'
                               )
                     )
                   }
                   else if( as.numeric(input$filechoice)==1)#input$kallisto_path!="" && 
                   {
                     req(input$kallisto_path)
                     fileInput(session$ns("file2"), label = h5('Choose Annotation file to upload'),
                               accept = c(
                                 'text/csv',
                                 'text/comma-separated-values',
                                 'text/tab-separated-values',
                                 'text/plain',
                                 '.csv',
                                 '.tsv'
                               )
                     )
                   }
                 })

  #compose count /expression table obtained as input to be displayed
  #edata reactive contains the count/expression table
  edata<-reactive({
    #setting up expression data
    #Get expression table from file
    
    if(as.numeric(input$filechoice)==2)
    {
      input_exp<-input_file(input$file1)
      if(!is.null(input_exp))
      {
        data<-input_exp[,-1]
        col_names<-colnames(data)
        print("line 248 module 1")
        print(head(data))
        #convert entries to integers
        data=as.matrix(data)
        storage.mode(data)="integer"
        data= data.frame(data)
        rownames(data)=as.character(input_exp[,1])
        colnames(data)<-col_names
        data<-data
      }
    }
    else if(as.numeric(input$filechoice)==1)
    {
      dat<-as.data.frame(txi()$counts)
      sample_names<-colnames(dat)
      #convert entries to integers
      data=as.matrix(dat)
      storage.mode(data)="integer"
      data= data.frame(data)
      rownames(data)=rownames(dat)
      colnames(data)<-sample_names
      print("module 1 line 271 ok")
      print(head(data))
      data <- data#[ rowSums(data) > 1, ]

    }

  })
  
  edata2 <- reactive({
    if(as.numeric(input$filechoice)==2)
    {
      input_exp<-input_file(input$file1)
      if(!is.null(input_exp))
      {
        data<-input_exp[,-1]
        col_names<-colnames(data)
        print("line 248 module 1")
        print(head(data))
        #convert entries to integers
        data=as.matrix(data)
        storage.mode(data)="integer"
        data= data.frame(data)
        rownames(data)=as.character(input_exp[,1])
        colnames(data)<-col_names
        data<-data
      }
    }
    else if(as.numeric(input$filechoice)==1)
    {
      data <- txi()
    }
  })

  #Compose annotation data from file
  #pdata contains annotation file
  pData<-reactive({
    #setting up annotation data
    #Get annotation table from file
    pheno<-input_file(input$file2)
    print("module 1 line 285 ok")
    print(pheno)

    #Get expression table
    data<-edata()
    #print(head(data))
    #Expression table and annotation table should not be null
    if(!is.null(data) && !is.null(pheno))
    {

      #Assuming that the first column of annotation table is sample id ,extract all sample IDs
      sample_id = pheno[,1]
      #print(sample_id)
      #Get all sample IDs from expression table(sample ID refer to column names of expression table)
      exp_sample_id = colnames(data)
      #Check if all sample ID in expression table are present in the annotation table
      if (all(exp_sample_id %in% sample_id))
      {
        #print("Yay")

        #set all variables of annotation table as factors
        col<-1:ncol(pheno)
        for (i in col)
        {
          pheno[,i]<-as.factor(pheno[,i])
        }
        #Remove those sample IDs that are present in the expression table but absent in the annotation table from the annotation table
        idx<-NULL
        if(!all(sample_id %in% exp_sample_id))
        {
          idx<-which(!(sample_id %in% exp_sample_id))
          pheno <- pheno[-idx, ]
        }

        pheno<-pheno

      }
      else 
        {
          pheno<-NULL
        }
      pheno
    }
  })
out<-list(file2=reactive({input$file2}),
          edata=reactive({edata()}),
          pData=reactive({pData()}),
          organism=reactive({input$organism}),
          edata2=reactive({edata2()}))#c(1,2,3,4)}))
  
  #input$file2}))#,edata=reactive({edata()}),pData=reactive({pData()}))
return(out)
  }