inst/shiny/server/server_07_differentialExpression.R

In compbiomed/BatchQC: Batch Effects Quality Control Software

### DIFFERENTIAL EXPRESSION ANALYSIS TAB ###
observeEvent(input$DE_batch, {
    req(reactivevalue$se, input$DE_batch)
    DE_covariate_choices <- covariates_not_confounded(reactivevalue$se,
        input$DE_batch)
    updateSelectizeInput(session = session, inputId = "DE_conditions",
        choices = DE_covariate_choices, selected = NULL)
})

observeEvent(input$DE_method, {
    req(reactivevalue$se, input$DE_batch)
    DE_covariate_choices <- covariates_not_confounded(reactivevalue$se,
        input$DE_batch)
    updateSelectizeInput(session = session, inputId = "DE_conditions",
        choices = DE_covariate_choices, selected = NULL)
})
observeEvent(input$DE_analyze, {
    req(reactivevalue$se, input$DE_analyze)

    # withProgress({
    #     setProgress(0.5, 'Calculating...')
    #     reactivevalue$DE_results <- DE_analyze(reactivevalue$se,
    #         input$DE_method, input$DE_batch, input$DE_conditions,
    #         input$DE_assay)
    #     setProgress(1, 'Complete!')
    # })

    withBusyIndicatorServer("DE_analyze", {
        reactivevalue$DE_results <- DE_analyze(reactivevalue$se,
                     input$DE_method, input$DE_batch, input$DE_conditions,
                     input$DE_assay)
        display_covariate <- names(reactivevalue$DE_results)[length(reactivevalue$DE_results)]

        output$DE_results <- renderDT({
            reactivevalue$DE_results[[length(reactivevalue$DE_results)]]
        })

        output$pval_summary <- renderDT({
            pval_summary(reactivevalue$DE_results)})

        output$pval_plot <- renderPlot({
            pval_plotter(reactivevalue$DE_results)
        })

        output$downloadDEData <- downloadHandler(
            filename = function() {
                paste("DE_results", ".csv", sep = "")
            },
            content = function(file) {
                write.csv(reactivevalue$DE_results[[length(reactivevalue$DE_results)]], file)
            }
        )

        updateSelectizeInput(session = session,
            inputId = "DE_res_selected",
            choices = names(reactivevalue$DE_results),
            selected = names(reactivevalue$DE_results)[length(
                reactivevalue$DE_results)])
        updateSelectizeInput(session = session,
            inputId = "result_to_view",
            choices = names(reactivevalue$DE_results),
            selected = names(reactivevalue$DE_results)[length(
                reactivevalue$DE_results)])
        updateSliderInput(session = session,
            inputId = "fcslider",
            min = round(min(abs(reactivevalue$DE_results[[length(reactivevalue$DE_results)]][, 1]))),
            max = round(max(abs(reactivevalue$DE_results[[length(reactivevalue$DE_results)]][, 1]))),
            value = round((max(abs(reactivevalue$DE_results[[length(reactivevalue$DE_results)]][, 1]))
                + min(abs(reactivevalue$DE_results[[length(reactivevalue$DE_results)]][, 1]))) / 2))
    })

})

plotVolcanoPlotButton <- eventReactive(input$volcano_plot, {
    volcano_plot(reactivevalue$DE_results[[as.character(input$DE_res_selected)]], input$pslider, input$fcslider)
})

output$volcano <- renderPlotly({
    plotVolcanoPlotButton()
})

observeEvent(input$DE_res_selected, {
    if (input$DE_res_selected != "") {
        updateSliderInput(session = session,
            inputId = "fcslider",
            min = 0,
            max = round(max(abs(reactivevalue$DE_results[[input$DE_res_selected]][, 1]))),
            value = round(median(abs(reactivevalue$DE_results[[input$DE_res_selected]][, 1]))))

    }
    })

observeEvent(input$result_to_view, {
    output$DE_results <- renderDT({
        reactivevalue$DE_results[[input$result_to_view]]
    })

    output$downloadDEData <- downloadHandler(
        filename = function() {
            paste(input$DE_method, "_results_", input$result_to_view, ".csv", sep = "")
        },
        content = function(file) {
            write.csv(reactivevalue$DE_results[[input$result_to_view]], file)
        }
    )
})