R/shinyGeneExon.R

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

#' Shiny Genes and Exons with nearby SNPs module
#'
#' Shiny module for scan1 analysis and plots, with interfaces \code{shinyGeneExonInput}, \code{shinyGeneExonUI} and  \code{shinyGeneExonOutput}.
#'
#' @param id identifier for shiny reactive
#' @param snp_par,chr_pos,top_snps_tbl,gene_exon_tbl,snp_action reactive arguments
#'
#' @author Brian S Yandell, \email{brian.yandell@@wisc.edu}
#' @keywords utilities
#' 
#' @return No return value; called for side effects.
#'
#' @export
#' @importFrom dplyr filter
#' @importFrom ggplot2 autoplot ggtitle
#' @importFrom shiny moduleServer NS reactive req 
#'   selectInput updateSelectInput
#'   dataTableOutput plotOutput uiOutput
#'   renderDataTable renderPlot renderUI
#'   fluidRow column
#'   withProgress setProgress
#'   downloadButton downloadHandler
#' @importFrom utils write.csv
#' @importFrom grDevices dev.off pdf
#' @importFrom rlang .data
#'   
shinyGeneExon <- function(id, snp_par, chr_pos, top_snps_tbl, gene_exon_tbl,
                          snp_action = shiny::reactive({"basic"})) {
  shiny::moduleServer(id, function(input, output, session) {
  ns <- session$ns
  
  pheno_names <- shiny::reactive({
    sort(unique(shiny::req(top_snps_tbl()$pheno)))
  })
  summary_gene_exon <- shiny::reactive({
    summary(shiny::req(gene_exon_tbl()),
            top_snps_tbl = shiny::req(top_snps_tbl()))
  })
  gene_names <- shiny::reactive({
    pheno_name <- shiny::req(snp_par$pheno_name)
    gene_in <- summary_gene_exon()
    if(nrow(gene_in)) {
      if(pheno_name %in% names(gene_in))
        gene_in <- gene_in[!is.na(gene_in[[pheno_name]]),]
      else
        return(NULL)
    }
    ## Order by decreasing LOD.
    if(nrow(gene_in))
      gene_in$gene[order(-gene_in[[pheno_name]])]
    else
      NULL
  })
  gene_exon_pheno <- shiny::reactive({
    pheno_name <- shiny::req(snp_par$pheno_name)
    gene_in <- gene_names()
    if(length(gene_in)) {
      subset(gene_exon_tbl(), gene_in)
    } else {
      NULL
    }
  })
  
  output$gene_sum <- shiny::renderDataTable({
    shiny::withProgress(message = 'Gene Exon Table ...', value = 0, {
      shiny::setProgress(1)
      summary_gene_exon()
    })
  }, options = list(scrollX = TRUE, pageLength = 5,
                    lengthMenu = list(c(5,10,20,-1),
                                      list("5","10","20","all"))))
  output$gene_name <- shiny::renderUI({
    selected <- input$gene_name
    choices <- gene_names()
    if(!isTruthy(selected %in% choices))
      selected <- choices[1]
    shiny::selectInput(ns("gene_name"), NULL,
                choices = choices,
                selected = selected)
  })
  observeEvent(gene_names(), {
    selected <- input$gene_name
    choices <- gene_names()
    if(!isTruthy(selected %in% choices))
      selected <- choices[1]
    shiny::updateSelectInput(session, "gene_name", NULL,
                choices = choices,
                selected = selected)
  })

  output$gene_plot <- shiny::renderPlot({
    if(is.null(input$gene_name)) {
      plot_null()
    } else {
      shiny::req(top_snps_tbl(), gene_exon_tbl(), gene_names())
      gene_name <- shiny::req(input$gene_name)
      pheno_name <- shiny::req(snp_par$pheno_name)
      shiny::withProgress(message = 'Gene Exon Plot ...', value = 0, {
        shiny::setProgress(1)
        plot_gene_exons(gene_exon_pheno(), 
                        dplyr::filter(top_snps_tbl(), .data$pheno == pheno_name),
                        gene_name, paste(pheno_name, snp_action()))
      })
    }
  })
  
  ## Outputs
  output$exon_input <- shiny::renderUI({
    switch(shiny::req(input$button),
           Plot    = shiny::uiOutput(ns("gene_name")))
  })
  output$exon_output <- shiny::renderUI({
    switch(shiny::req(input$button),
           Plot    = shiny::plotOutput(ns("gene_plot")),
           Summary = shiny::dataTableOutput(ns("gene_sum")))
  })
  
  ## Downloads.
  output$downloadData <- shiny::downloadHandler(
    filename = function() {
      file.path(paste0("gene_exon_", chr_pos(), "_", snp_action(), ".csv")) },
    content = function(file) {
      utils::write.csv(shiny::req(summary_gene_exon()), file)
    }
  )
  output$downloadPlot <- shiny::downloadHandler(
    filename = function() {
      file.path(paste0("gene_exon_", chr_pos(), "_", snp_action(), ".pdf")) },
    content = function(file) {
      gene_exon <- shiny::req(gene_exon_pheno())
      pheno_name <- shiny::req(snp_par$pheno_name)
      top_snps <- dplyr::filter(shiny::req(top_snps_tbl()), .data$pheno == pheno_name)
      grDevices::pdf(file, width = 9)
      for(gene_name in shiny::req(gene_names())) {
        print(plot_gene_exons(gene_exon, top_snps,
                              gene_name, pheno_name))
      }
      grDevices::dev.off()
    }
  )
  output$select <- shiny::renderUI({
    shiny::selectInput(ns("button"), NULL, c("Plot","Summary"),
                input$button)
  })
})
}
shinyGeneExonInput <- function(id) {
  ns <- shiny::NS(id)
  shiny::fluidRow(
    shiny::uiOutput(ns("select")),
    shiny::uiOutput(ns("exon_input")))
}
shinyGeneExonUI <- function(id) {
  ns <- shiny::NS(id)
  shiny::fluidRow(
    shiny::column(6, shiny::downloadButton(ns("downloadData"), "CSV")),
    shiny::column(6, shiny::downloadButton(ns("downloadPlot"), "Plots")))
}
shinyGeneExonOutput <- function(id) {
  ns <- shiny::NS(id)
  shiny::uiOutput(ns("exon_output"))
}