inst/shiny/server/server_profiler.R

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

output$covars <- shiny::renderTable({
  vals$covars
}, colnames = FALSE)

output$assays <- shiny::renderTable({
  vals$datassays
}, colnames = FALSE)

shiny::observeEvent(input$runprofiler, {
  output$visdat <- DT::renderDataTable(
    head(as.data.frame(SummarizedExperiment::colData(vals$profilerdat))),
    options = list(scrollX = TRUE)
  )
})

shiny::observeEvent(input$mkassay, {
  if (input$newassay == "log") {
    vals$tbdat <- mkAssay(vals$tbdat, input_name = "counts",
                          log = TRUE, counts_to_CPM = FALSE)
    vals$datassays <- names(SummarizedExperiment::assays(vals$tbdat))
  } else if (input$newassay == "cpm") {
    vals$tbdat <- mkAssay(vals$tbdat, input_name = "counts")
    vals$datassays <- names(SummarizedExperiment::assays(vals$tbdat))
  } else if (input$newassay == "logcpm") {
    vals$tbdat <- mkAssay(vals$tbdat, input_name = "counts", log = TRUE)
    vals$datassays <- names(SummarizedExperiment::assays(vals$tbdat))
  }
})

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

shiny::observeEvent(input$runprofiler, {
  vals$profilerdat <- shiny::isolate(
    runTBsigProfiler(vals$tbdat,
                     useAssay = input$profassay,
                     signatures = TBsignatures,
                     algorithm = input$profalg,
                     combineSigAndAlgorithm = TRUE,
                     parallel.sz = 4,
                     update_genes = FALSE))
})

shiny::observeEvent(input$runprofiler, {
  output$allheat <- NULL
  output$indheat <- NULL
  output$boxplotind <- NULL
  output$heatcomp <- NULL
  output$bootbox <- NULL
  output$rocsep <- NULL
})