inst/app/server.R

In vjcitn/tnt4dn8: TnT applications with GWAS in dn8 format

library(shiny)
library(tnt4dn8)

#' demo server
#' @importFrom shinytoastr toastr_info
#' @importFrom TnT renderTnT
server = function(input, output, session) {
  build_gt = reactive({
    shinytoastr::toastr_info("building global gene models...")
    txdb38 = GenomeInfoDb::keepStandardChromosomes(TxDb.Hsapiens.UCSC.hg38.knownGene)
    tt = TnT::TxTrackFromTxDb(txdb38, height=400, color="darkred", seqlevel="chr20")
    GT = TnT::GeneTrackFromTxDb(txdb38, height=100, color="darkgreen", seqlevel="chr20")
    list(tt=tt, GT=GT)
    })
  output$gname = renderPrint({
    cat(paste(input$gene, "in GTEx Lung."))
  })
  output$tntmanh = TnT::renderTnT({
   shinytoastr::toastr_info("filtering annotations...", position="top-center")
   sym = input$gene
   rad = input$radius
   data(gtex_b38_lung_chr20_exc)
   data(limgwcat_b38)
   tab = gtex_b38_lung_chr20_exc |> filter_sym(sym, radius=rad) |> as.data.frame()
   tab2 = limgwcat_b38 |> filter_sym(sym, radius=rad) |> as.data.frame()
   bgt = build_gt()
   tntplot3(tab, tab2, tt=bgt$tt, GT=bgt$GT, lab1="GTEx Lung", lab2="EBI GWASCAT")
  })
  output$desc = renderPrint({
   packageDescription("tnt4dn8")
  })
  output$eqtltab = DT::renderDataTable({
   sym = input$gene
   rad = input$radius
   data(gtex_b38_lung_chr20_exc)
   gtex_b38_lung_chr20_exc |> filter_sym(sym, radius=rad) |> as.data.frame()
  })
  output$gwastab = DT::renderDataTable({
   sym = input$gene
   rad = input$radius
   data(limgwcat_b38)
   limgwcat_b38 |> filter_sym(sym, radius=rad) |> as.data.frame()
  })
  observeEvent(input$stopBtn, {
    stopApp(NULL)
    })
}