plotGatingHierarchy: plotGatingHierarchy

In VoisinneG/flowR: R-shiny interface for the analysis of flow cytometry data

Description

A shiny Module to plot a gating hierarchy

Usage

plotGatingHierarchy(
  input,
  output,
  session,
  rval,
  plot_params = reactiveValues()
)

Arguments

input	shiny input
output	shiny output
session	shiny session
rval	a reactivevalues object with the following elements : gating_set : a GatingSet object apply_trans : logical; apply transformations defined in rval$gating_set apply_comp : logical; apply compensation defined in rval$gating_set
plot_params	A reactiveValues object with plot parameters

Value

A list of plots

Examples

## Not run: 
library(shiny)
library(shinydashboard)
library(flowWorkspace)
library(flowCore)

if (interactive()){

  ui <- dashboardPage(
    dashboardHeader(title = "plotGatingHierarchy"),
    sidebar = dashboardSidebar(disable = TRUE),
    body = dashboardBody(
      fluidRow(
        column(12, box(width = NULL, simpleDisplayUI("simple_display_module")))
      )
    )
  )

  server <- function(input, output, session) {

    rval <- reactiveValues()
    plot_params <- reactiveValues()
    display_params <- reactiveValues()
    
    observe({
      gs <- load_gs("./inst/ext/gs")
      rval$gating_set <- gs
      plot_params$sample <- pData(gs)$name
      plot_params$plot_type <- "hexagonal"
      display_params$top <- paste(plot_params$sample, collapse = " + ") 
    })

    plot_all_gates <- callModule(plotGatingHierarchy, "module",
                      rval = rval,
                      plot_params = plot_params)

    callModule(simpleDisplay, "simple_display_module", 
               plot_list = plot_all_gates, params = display_params)

  }

  shinyApp(ui, server)

}

## End(Not run)

VoisinneG/flowR documentation built on June 1, 2021, 6:42 p.m.