plateCore (version 1.30.0)

xyplot: Scatter plots (dotplots) for flowPlates.

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

"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

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)