plotCytoUI: Build plots from a GatingSet

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

Description

Build plots from a GatingSet

plotCyto module server function

Usage

plotCytoUI(id)

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

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
use_ggcyto	logical, use the ggcyto package to generate plots

Value

A reactivevalues object with the following elements :

plot

a plot or a list of plots

params

plot parameters

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