inst/shiny/server/server_visualization.R

In compbiomed/TBSignatureProfiler: Profile RNA-Seq Data Using TB Pathway Signatures

shiny::observe({
  if (is.null(vals$profilerdat)) {
    shinyWidgets::updatePickerInput(session, "selectsigs", choices = NULL)
  } else {
    shiny::isolate(
      shinyWidgets::updatePickerInput(
        session, "selectsigs", choices = subset(
          siglist,
          siglist %in% colnames(
            SummarizedExperiment::colData(vals$profilerdat))),
        selected = subset(
          siglist, siglist %in% colnames(
            SummarizedExperiment::colData(vals$profilerdat)))))
  }
})

shiny::observe({
  shiny::updateSelectInput(session, "allheatcovar", choices = vals$covars)
})

shiny::observeEvent(input$allheatplot, {
  output$allheat <- shiny::renderPlot({
    colors <- RColorBrewer::brewer.pal(6, "Spectral")
    col_me <- circlize::colorRamp2(base::seq(from = -2, to = 2,
                                             length.out = 6), colors)
    shiny::isolate({
      signatureHeatmap(
        vals$profilerdat, name = "Heatmap of Signatures",
        signatureColNames = names(TBsignatures[input$selectsigs]),
        annotationColNames = input$allheatcovar, scale = TRUE,
        showColumnNames = TRUE, choose_color = col_me)
    })
  })
})

shiny::observe({
  shiny::updateSelectInput(session, "singheatcovar", choices = vals$covars)
})

shiny::observe({
  if (is.null(vals$profilerdat)) {
    shinyWidgets::updatePickerInput(session, "singheat", choices = NULL)
  } else {
    shinyWidgets::updatePickerInput(
      session, "singheat", choices = subset(
        siglist, siglist %in% colnames(
          SummarizedExperiment::colData(vals$profilerdat))))
  }
})

shiny::observe({
  shinyWidgets::updatePickerInput(session, "genes",
                                  choices = TBsignatures[input$singheat],
                                  selected = TBsignatures[[input$singheat]])
  })

shiny::observeEvent(input$singheatplot, {
  output$indheat <- shiny::renderPlot({
    shiny::isolate({
      print(signatureGeneHeatmap(inputData = vals$profilerdat,
                                 useAssay = input$profassay,
                                 input$genes,
                                 signatureColNames = input$singheat,
                                 annotationColNames = input$singheatcovar,
                                 showColumnNames = TRUE))
      })
    })
  })

shiny::observe({
  if (is.null(vals$profilerdat)) {
    shinyWidgets::updatePickerInput(session, "singbox", choices = NULL)
  } else {
    shinyWidgets::updatePickerInput(
      session, "singbox", choices = subset(
        siglist, siglist %in% colnames(colData(vals$profilerdat))))
  }
})

shiny::observe({
  shiny::updateSelectInput(session, "singboxcovar",
                                  choices = vals$covars)
})

shiny::observeEvent(input$singboxplot, {
  output$boxplotind <- shiny::renderPlot({
    shiny::isolate({
      print(signatureBoxplot(vals$profilerdat,
                             signatureColNames = input$singbox,
                             annotationColName = input$singboxcovar))
    })
  })
})

shiny::observe({
  if (is.null(vals$profilerdat)) {
    shiny::updateSelectInput(session, "singcomp", choices = NULL)
  } else {
    shiny::updateSelectInput(
      session, "singcomp", choices = subset(
        siglist, siglist %in% colnames(
          SummarizedExperiment::colData(vals$profilerdat))))
  }
})

shiny::observe({
  shiny::updateSelectInput(session, "compassay", choices = vals$datassays)
})

shiny::observe({
  shiny::updateSelectInput(session, "compcovar", choices = vals$covars)
})

shiny::observeEvent(input$compplot, {
  output$heatcomp <- shiny::renderPlot({
    shiny::isolate({
      suppressWarnings(compareAlgs(vals$profilerdat,
                                   annotationColName = input$compcovar,
                                   scale = TRUE,
                                   algorithm = input$compalg,
                                   useAssay = input$compassay,
                                   signatures = TBsignatures[input$singcomp],
                                   show.pb = TRUE))
    })
  })
})