R/shinyPhenoPlot.R

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

#' Shiny Phenotype Plot module
#'
#' Shiny module to plot phenotypes, with interface \code{shinyPhenoPlotUI}.
#'
#' @param id identifier for shiny reactive
#' @param set_par,phe_mx,cov_df reactive arguments
#'
#' @author Brian S Yandell, \email{brian.yandell@@wisc.edu}
#' @keywords utilities
#'
#' @return 2-element vector of scan window
#'
#' @export
#' @importFrom shiny moduleServer NS 
#'   plotOutput dataTableOutput
#'   renderPlot renderDataTable
#'   tagList
#'   withProgress setProgress
#' @importFrom dplyr mutate
#' @importFrom ggplot2 ggplot aes_string geom_density geom_rug
#' @importFrom GGally ggscatmat
shinyPhenoPlot <- function(id, set_par, phe_mx, cov_df) {
  shiny::moduleServer(id, function(input, output, session) {
  ns <- session$ns
  
  ## Scatter plot or density
  output$phe_sum <- shiny::renderDataTable({
    shiny::req(phe_mx())
    shiny::withProgress(message = 'Pheno Summary ...', value = 0, {
      shiny::setProgress(1)
      summary_na(phe_mx())
    })
  }, escape = FALSE, 
  options = list(scrollX = TRUE, 
                 pageLength = 5,
                 lengthMenu = list(c(5,10,-1), c(5,10,"all"))))
  output$phePlot <- shiny::renderPlot({
    # If no df, gives blank area.
    # Better to either do nothing or do plot_null()
    # use uiOutput and renderUI?
    if(!shiny::isTruthy(set_par$pheno_names))
      return(plot_null("need to\nChoose phenotype"))
    shiny::withProgress(message = 'Pheno Plot ...', value = 0, {
      shiny::setProgress(1)
      plot_sex(phe_mx(), cov_df())
    })
  })
  output$phePlotTable <- shiny::renderUI({
    shiny::tagList(
      shiny::plotOutput(ns("phePlot")),
      shiny::dataTableOutput(ns("phe_sum")))
  })
})
}

shinyPhenoPlotUI <- function(id) {
  ns <- shiny::NS(id)
  shiny::uiOutput(ns("phePlotTable"))
}