xyplot-methods: Scatter plots (dotplots) for flowPlates.

In plateCore: Statistical tools and data structures for plate-based flow cytometry

Description

A function to create dotplots, and smoothed scatter plots, from flowPlates. This function is a slightly modified version of xyplot from flowViz. The flowPlate xyplot allows users to overlay plots of test samples versus controls, and makes creating informative flowStrips easier. Refer to the documentation for xyplot from flowViz and lattice for more detailed information.

Usage

## S4 method for signature 'formula,flowPlate'
xyplot(x, data, xlab, ylab,
				as.table = TRUE,
				prepanel = prepanel.xyplot.flowPlate,
				panel = panel.xyplot.flowPlate,
				pch = ".", smooth = TRUE,
				filter = NULL,
				filterResults = NULL,
				displayFilter = TRUE,
				flowStrip=NULL,
				flowStripCex=1,
				strip=function(...,style=1) strip.default(...,style=1),
				...)

Arguments

x	A formula describing the layout of the plots. Plots for flowPlates usually condition on either as.factor(name) or as.factor(Well.Id) since only one flowFrame can be shown on each panel (with the exception of Negative.Control overlays).
data	A flowPlate.
xlab	Label for x-axis.
ylab	Label for y-axis.
as.table	Defaults to table layout.
prepanel	Lattice-flowViz prepanel function.
panel	Lattice-flowViz panel function.
pch	Plotting character.
smooth	Plot a smoothed scatterplot by default.
filter	A flowCore filter to apply to each flowFrame.
filterResults	If filterResults="Negative.Control", the negative control wells corresponding to a test well are overlayed in the test well plots.
displayFilter	Defaults to displaying filter on the plot.
flowStrip	Character vector indicating additional information to be printed on the strip. Values can include any combination of "Well.Id","MFI","MFI.Ratio", and "Percent.Positive".
flowStripCex	Font size for the flowStrip.
strip	Lattice strip function.
...	Optional arguments

Author(s)

Errol Strain

See Also

flowViz::xyplot

Examples

library(plateCore)
data(plateCore)

# Create a flowPlate from the sample data in plateCore
fp <- flowPlate(pbmcPlate,wellAnnotation,plateName="P1")

## Create a rectangle filter
rectGate <- rectangleGate("FSC-H"=c(300,700),"SSC-H"=c(50,400))

xyplot(`SSC-H` ~ `FSC-H` | as.factor(name), 
	fp[1], smooth=FALSE, filter=rectGate, displayFilter=FALSE)

plateCore documentation built on May 6, 2019, 2:41 a.m.