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

In ggcyto: Visualize Cytometry data with ggplot

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 is called on 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

## 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 gs_get_pop_paths)

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")

#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 Nov. 8, 2020, 5:30 p.m.