R/shinySNPFeature.R

In byandell/qtl2shiny: Shiny interface for 'qtl2' Fine Mapping

#' Shiny SNP Features in SNP Region module
#'
#' Shiny module for scan1 analysis and plots, with interfaces \code{shinySNPFeatureInput}, \code{shinySNPFeatureUI} and  \code{shinySNPFeatureOutput}.
#'
#' @param id identifier for shiny reactive
#' @param snp_par,chr_pos,snp_scan_obj,top_snps_tbl,snpinfo,gene_exon_tbl,snp_action reactive arguments
#'
#' @author Brian S Yandell, \email{brian.yandell@@wisc.edu}
#' @keywords utilities
#'
#' @export
#' @importFrom dplyr distinct
#' @importFrom qtl2pattern merge_feature
#' @importFrom ggplot2 autoplot
#' @importFrom shiny moduleServer NS reactive req 
#'   selectInput
#'   dataTableOutput plotOutput uiOutput
#'   renderDataTable renderPlot renderUI
#'   fluidRow column tagList
#'   withProgress setProgress
#'   downloadButton downloadHandler
#' @importFrom utils write.csv
#' @importFrom grDevices dev.off pdf   
#'   
shinySNPFeature <- function(id, snp_par, chr_pos, snp_scan_obj, snpinfo,
                            top_snps_tbl, gene_exon_tbl, 
                            snp_action = shiny::reactive({"basic"})) {
  shiny::moduleServer(id, function(input, output, session) {
  ns <- session$ns

  top_feature <- shiny::reactive({
    shiny::req(top_snps_tbl(), snp_scan_obj(), snpinfo(), gene_exon_tbl())
    shiny::withProgress(message = 'Merging gene info ...', value = 0,
    {
      shiny::setProgress(1)
      topSNPs(top_snps_tbl(), snpinfo(),
              snp_scan_obj(), gene_exon_tbl(),
              snp_par$pheno_name)
    })
  })
  output$top_snp_type <- shiny::renderDataTable({
    tops <- shiny::req(top_feature(), "SNP type")
    summary(tops)
  }, options = list(scrollX = TRUE, paging = FALSE, searching=FALSE))
  output$top_pattern <- shiny::renderDataTable({
    summary(top_feature(), "pattern")
  }, options = list(scrollX = TRUE, paging = FALSE, searching=FALSE))
  phename <- shiny::reactive({dimnames(snp_scan_obj())[[2]]})
  output$top_gene_by_snp <- shiny::renderPlot({
    shiny::req(top_feature(), snp_par$pheno_name)
    ggplot2::autoplot(top_feature(), snp_par$pheno_name, "consequence")
  })
  output$top_gene_by_pattern <- shiny::renderPlot({
    shiny::req(top_feature(), snp_par$pheno_name)
    ggplot2::autoplot(top_feature(), snp_par$pheno_name, "pattern")
  })
  output$by_choice <- shiny::renderUI({
    switch(input$by_choice,
           Pattern = {
             shiny::tagList(
               shiny::plotOutput(ns("top_gene_by_snp")),
               shiny::dataTableOutput(ns("top_pattern")))
           },
           Consequence = {
             shiny::tagList(
               shiny::plotOutput(ns("top_gene_by_pattern")),
               shiny::dataTableOutput(ns("top_snp_type")))
           })
  })
  
  ## Downloads.
  output$downloadData <- shiny::downloadHandler(
    filename = function() {
      file.path(paste0("top_feature_", chr_pos(), "_", snp_action(), ".csv")) },
    content = function(file) {
      utils::write.csv(shiny::req(top_feature()), file)
    }
  )
  ## This does not work as items below do not exist.
  output$downloadPlot <- shiny::downloadHandler(
    filename = function() {
      file.path(paste0("top_feature_", chr_pos(), "_", snp_action(), ".pdf")) },
    content = function(file) {
      shiny::req(top_feature())
      grDevices::pdf(file, width = 9)
      for(phenoi in phename()) {
        print(ggplot2::autoplot(top_feature(), phenoi, "consequence"))
        print(ggplot2::autoplot(top_feature(), phenoi, "pattern"))
      }
      grDevices::dev.off()
    }
  )
})
}

shinySNPFeatureInput <- function(id) {
  ns <- shiny::NS(id)
  shiny::selectInput(ns("by_choice"), NULL, 
              c("Pattern","Consequence"))
}
shinySNPFeatureUI <- function(id) {
  ns <- shiny::NS(id)
  shiny::fluidRow(
    shiny::column(6, shiny::downloadButton(ns("downloadData"), "CSV")),
    shiny::column(6, shiny::downloadButton(ns("downloadPlot"), "Plots")))
}
shinySNPFeatureOutput <- function(id) {
  ns <- shiny::NS(id)
  shiny::uiOutput(ns("by_choice"))
}