geom_overlay: Overlay a population on an existing ggcyto plot analogous to...

In ggcyto: Visualize Cytometry data with ggplot

Description

It is useful for "backgating" plots.

Usage

geom_overlay(data, ...)

Arguments

data	a filter (Currently only rectangleGate (1d or 2d), polygonGate, ellipsoidGate are supported.) or a list of these gates or filterList or character specifying a gated cell population in the GatingSet
...	other arguments mapping, The mapping aesthetic mapping data a polygonGate fill polygonGate is not filled by default colour default is red pd pData (data.frame) that has rownames represents the sample names used as key to be merged with filterList

Value

a geom_overlay layer

Examples

library(ggcyto)
dataDir <- system.file("extdata",package="flowWorkspaceData")
gs <- load_gs(list.files(dataDir, pattern = "gs_manual",full = TRUE))
p <- autoplot(gs, "CD3+")

# add a flowSet as the overlay
fs <- gs_pop_get_data(gs, "DPT")
p + geom_overlay(data = fs, size = 0.3, alpha = 0.7)

# add overlay layer by gate name
p + geom_overlay(data = "DNT", size = 0.3, alpha = 0.7)

#add overlay for 1d densityplot
p <- ggcyto(gs, aes(x = CD4), subset = "CD3+") + geom_density(aes(y = ..count..))
p + geom_overlay("DNT", aes(y = ..count..), fill = "red")

Example output

Loading required package: ggplot2
Loading required package: flowCore
Loading required package: ncdfFlow
Loading required package: RcppArmadillo
Loading required package: BH
Loading required package: flowWorkspace
As part of improvements to flowWorkspace, some behavior of
GatingSet objects has changed. For details, please read the section
titled "The cytoframe and cytoset classes" in the package vignette:

  vignette("flowWorkspace-Introduction", "flowWorkspace")
Coordinate system already present. Adding new coordinate system, which will replace the existing one.

ggcyto documentation built on Nov. 8, 2020, 5:30 p.m.