autoplot: Plot cytometry data in one or two dimension with the ggcyto...

Description Usage Arguments Value Examples

Description

Overloaded autoplot methods for the cytometry data structure: flowFrame or flowSet, Gatinghierarchy, GatingSet. It plots the cytometry data with geom_histogram, geom_density or geom_hex. When autoplot a GatingSet/Gatinghierarchy, the second argument should be a gate or population node. And the dimensions(channels/markers) are deduced from the gate dimensions.

Usage

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## S3 method for class 'flowSet'
autoplot(object, x, y = NULL, bins = 30, ...)

## S3 method for class 'ncdfFlowList'
autoplot(object, ...)

## S3 method for class 'flowFrame'
autoplot(object, x, ...)

## S3 method for class 'GatingSetList'
autoplot(object, ...)

## S3 method for class 'GatingSet'
autoplot(object, gate, x = NULL, y = "SSC-A",
  bins = 30, axis_inverse_trans = TRUE, ...)

## S3 method for class 'GatingHierarchy'
autoplot(object, gate, y = "SSC-A",
  bool = FALSE, arrange.main = sampleNames(object), arrange = TRUE,
  merge = TRUE, projections = list(), strip.text = c("parent",
  "gate"), path = "auto", ...)

Arguments

object

The data source. A core cytometry data structure. A flowFrame, flowSet, GatingSet or GatingHierarchy object

x

define the x dimension of the plot (not used when object is a GatingSet). When object is a flowFrame, it can be missing, which plots 1d density plot on all the channels.

y

define the y dimension of the plot. Default is NULL, which means 1d densityplot.

bins

passed to geom_hex

...

other arguments passed to ggplot

gate

the gate to be plotted

axis_inverse_trans

logical flag indicating whether to add axis_x_inverse_trans and axis_x_inverse_trans layers.

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

path

the gating path format (passed to getNodes)

Value

a ggcyto object

Examples

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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")

#1d- density plot on all channels
autoplot(fs[[1]])

#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+")
#display axis values in transformed scale
autoplot(gs, "CD3+", axis_inverse_trans = FALSE)

#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")

ggcyto documentation built on Jan. 15, 2019, 6:01 p.m.