ggcyto (version 1.0.5)

autoplot.flowSet: Plot fluorescence intensity in one or two dimension.

Description

Overloaded autoplot for the cytomertry data structure: flowFrame or flowSet, Gatinghierarchy, GatingSet. It plots the cytometry data with geom_histogram, geom_density or geom_hex.

Usage

"autoplot"(object, x, y = NULL, bins = 30, ...)
"autoplot"(object, ...)
"autoplot"(object, gate, x = NULL, y = "SSC-A", bins = 30, ...)
"autoplot"(object, gate, y = "SSC-A", bool = FALSE, arrange.main = sampleNames(object), arrange = TRUE, merge = TRUE, projections = list(), strip.text = c("parent", "gate"), ...)

Arguments

object

flowFrame, flowSet, GatingSet object

x,y

define the dimension of the plot

bins

passed to geom_hex

...

other arguments passed to ggplot

gate

the gate to be plotted

bool

whether to plot boolean gates

arrange.main

the main title of the arranged plots

arrange

whether to use arrangeGrob to put multiple plots in the same page

merge

wehther to merge multiple gates into the same panel when they share the same parent and projections

projections

a list of customized projections

strip.text

either "parent" (the parent population name) or "gate "(the gate name). The latter usually is used when merge is FALSE

Value

a ggcyto object

Examples

library(flowCore)
data(GvHD)
fs <- GvHD[subset(pData(GvHD), Patient %in%5:7 & Visit %in% c(5:6))[["name"]]]

#1d- density plot
autoplot(fs, x = "SSC-H")

#2d plot: default geom_hex plot
autoplot(fs, x = 'FSC-H', y ='SSC-H')

#autplot for GatingSet
dataDir <- system.file("extdata",package="flowWorkspaceData")
gs <- load_gs(list.files(dataDir, pattern = "gs_manual",full = TRUE))
autoplot(gs, "CD3+")

#autplot for GatingHierarchy
gh <- gs[[1]]
autoplot(gh) # by default the strip.text shows the parent population

#To display the gate name
#autoplot(gh , strip.text = "gate")