plotGatingSetInput: Build plots from a GatingSet

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

Description

Build plots from a GatingSet

plotGatingSet module server function

Usage

plotGatingSetInput(id)

plotGatingSet(
  input,
  output,
  session,
  rval,
  plot_params = reactiveValues(),
  simple_plot = TRUE,
  auto_update = TRUE,
  show_gates = FALSE,
  polygon_gate = NULL
)

Arguments

id	shiny id
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	reactivevalues object used to initialize plot parameters. Amongst others it can contain the following elements (not mandatory): plot_type : type of plot sample : names of samples subset : names of subsets xvar : x-axis variables yvar : y-axis variables color_var : color aesthetic group_var : group aesthetic facet_var : variable used to show different plot facets split_var : variable used to create multiple plots
simple_plot	logical, disable a number of plot options (such as faceting, multiple plots with different x, y or color variables)
auto_update	Should plot update be automatic? If FALSE, plot update is controlled by an action button.
show_gates	Should gates with coordinates matching plot coordinates be displayed
polygon_gate	a reactiveValues object with polygon coordinates to be plotted as an additionnal layer. Must contain elements : x vector of x coordinates y vector of y coordinates

Value

A reactivevalues object with the following elements :

plot

a plot or a list of plots

params

plot parameters

Examples

## Not run: 
library(shiny)
library(shinydashboard)
library(flowWorkspace)
library(flowCore)
library(viridis)
library(scales)
library(ggplot2)
library(ggrepel)
library(plotly)
library(ggridges)

if (interactive()){
  
  ui <- dashboardPage(
    dashboardHeader(title = "plotGatingSet"),
    sidebar = dashboardSidebar(disable = TRUE),
    body = dashboardBody(
      fluidRow(
        column(4, box(width = NULL, plotGatingSetInput("module"))),
        column(8, box(width = NULL, simpleDisplayUI("simple_display_module")))
      )
    )
  )
  
  server <- function(input, output, session) {
    
    rval <- reactiveValues()
    plot_params <- reactiveValues()
    
    observe({
      utils::data("GvHD", package = "flowCore")
      rval$gating_set <- GatingSet(GvHD)
      plot_params$plot_type <- "histogram"
    })
    
    res <- callModule(plotGatingSet, "module",
                      rval = rval,
                      plot_params = plot_params)
    
    callModule(simpleDisplay, "simple_display_module", res$plot)
    
  }
  
  shinyApp(ui, server)
  
}
## End(Not run)

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