server-enrich.R

#server-enrich.R

EnrichRun <- reactiveValues(EnrichRunValue = FALSE) # to precise the run button has not been clicked


output$enrichparDEGs <- renderUI({    # set of parameters
    radioButtons(
      'selectDEGs',
      'Select DEGs from your original DEA ?',
      choices = c('yes','no'),
      selected = 'no')
})

output$enrichpar_filter_DEGs <- renderUI({    # set of parameters
  radioButtons(
    'selectfilterDEGs',
    'Select DEGs from your filtered DEA (for MA/Volcano) ?',
    choices = c('yes','no'),
    selected = 'no')
})

observeEvent(input$selectDEGs,{
  if (input$selectDEGs == 'yes'){
    data_selec <- as.vector(var$genelist)
    updateTextAreaInput(
      session = getDefaultReactiveDomain(),
      "list_ids",
      "Paste Gene List",
      value = data_selec
    )
  }else{
    updateTextAreaInput(
      session = getDefaultReactiveDomain(),
      "list_ids",
      "Paste Gene List",
      placeholder = 'paste your gene set separated by "," '
    )
  }
})

observeEvent(input$selectfilterDEGs,{
if (input$selectfilterDEGs == "yes"){
  data_selec <- as.vector(var$filter_genelist)
  updateTextAreaInput(
    session = getDefaultReactiveDomain(),
    "list_ids",
    "Paste Gene List",
    value = data_selec
  )
}else{
  updateTextAreaInput(
    session = getDefaultReactiveDomain(),
    "list_ids",
    "Paste Gene List",
    placeholder = 'paste your gene set separated by "," '
  )
}
})


observeEvent(input$enrichmentgo,{  # when the button is clicked
  progressSweetAlert(              # progress bar
    session = session,
    id = "enrichProgress",
    title = "Work in progress",
    display_pct = TRUE,
    value = 0
  )


    geneset <-unlist(strsplit(input$list_ids, split = ',')) # takes the gene set



  updateProgressBar(              # update progress bar
    session = session,
    id = "enrichProgress",
    title = "Enrichment in progress...",
    value = 50
  )

  enrichement <- unlist(strsplit(input$chosenEnrich, split = '\n'))
  res <- gost(geneset,
              organism = input$inputorg,
              ordered_query = T,
              user_threshold = input$userpval_cutoff,
              correction_method = input$correction,
              domain_scope = input$chosenscope,
              sources = enrichement,
              significant = F)




  updateProgressBar(           # updating the progress bar
    session = session,
    id = "enrichProgress",
    title = "Enrichement in progress...",
    value = 75
  )

  res_enrich <- as.data.frame(res$result)# result as data frame
  res_enrich <- res_enrich[,-1]
  res_enrich <- res_enrich[order(res_enrich[,2]),]
  res_enrich <- res_enrich[1:as.numeric(input$topres_enrich),]
  res_enrich <- res_enrich[,-1]
  res_enrich <- res_enrich[,-2]
  res_enrich <- res_enrich[,-2]
  res_enrich <- res_enrich[,-2]
  res_enrich <- res_enrich[,-2]
  res_enrich <- res_enrich[,-2]
  res_enrich <- res_enrich[,-5]
  res_enrich <- res_enrich[,-5]


  output$EnrichResultTable <-  DT::renderDataTable({   # result table
    enrich_data <- res_enrich
    colnames(enrich_data) <- c("P Value","Term_id", "Enrichment","Term_name", "Parents")
    DT::datatable(
      enrich_data,
      extensions = 'Buttons',    # download button
      option = list(
        paging = TRUE,
        searching = TRUE,
        fixedColumns = TRUE,
        autoWidth = TRUE,
        ordering = TRUE,
        dom = 'Bfrtip',
        buttons = list(list(
          extend = 'collection',
          buttons = list(extend='csv',
                         filename = "results_enrichment"),
          text = 'Download')),
        scrollX = TRUE,
        pageLength = 10,
        searchHighlight = TRUE,     # search bar
        orderClasses = TRUE

      ),

      class = "display")
  }, server = FALSE)

  EnrichRun$EnrichRunValue <- input$enrichmentgo   # precise the run button has been clicked
  updateNavbarPage(session, "entabs", "redirectres") # redirection to the result table after the enrichment is done

  closeSweetAlert(session = session)        # close alert that the enrichment is done
  sendSweetAlert(session = session,
                 title = "DONE",
                 text = "Enrichment was successfully performed.",
                 type = "success")

  ##########

  output$distribenrich <- renderPlotly({     # bar chart of results using plotly  : term with respect of -log(p-value)
    p <- gostplot(res,
                  capped = T,
                  interactive = TRUE
                  )

    p
  })


  output$EnrichBarPlot <- renderPlotly({
    fig <- plot_ly(
      res_enrich,
      x = ~(-log(p_value)),
      y = ~term_name,
      type = "bar",
      color = ~factor(source)

    )
    fig
  })

})

output$EnrichParams <- renderUI({
  if(AnalysisRun$AnalysisRunValue){    # if the calculation is done then show the params with DEGs
      uiOutput('enrichparDEGs')
  }
})

output$EnrichfiltParams <- renderUI({
if (FilterRun$FilterRunValue){
  uiOutput('enrichpar_filter_DEGs')
}
})


# result table render

output$EnrichResults <- renderUI({
  if(EnrichRun$EnrichRunValue){   # if the run button has been clicked, then show the results
    tagList(
      fluidRow(
        column(12, plotlyOutput("distribenrich") %>% withSpinner()),
        column(12, dataTableOutput('EnrichResultTable') %>% withSpinner())
      ))
    } else {                 # if not message to do it
        helpText("Run Enrichment to obtain the Result Table.")
      }
})

output$EnrichBar <- renderUI({
  if(EnrichRun$EnrichRunValue){
    tagList(
      fluidRow(
        column(12, plotlyOutput("EnrichBarPlot") %>% withSpinner())
      )
    )
  }else{
    helpText(("Run Enrichment to obtain the Result Table."))
  }
})