overlay: 'overlay' create a layer on an existing volcano plot

In harrig12/pointszr: Point Resizing for Volcano Plots

Description

overlay should be executed after vplot(), and can be re-executed
several times to build up layers on a plot.

Usage

overlay(DDSresult, szMod = 0.5, pch = 20, labelPoints = FALSE, ...)

addLabels(DDSresult, pos = 3, labels = rownames(DDSresult), ...)

Arguments

DDSresult	a DESeqResults object
szMod	sizing modifier, a numerical vector to be applied to the elements of DDSResult. Vectors shorter than the axis they're being applied to will be recycled.
pch	point style to be displayed.
labelPoints	boolean, whether to label the points from DDSresult using addLabels.
...	additional arguments to pass to par
pos	label position relative to point
labels	names for points

Details

addLabels will add point labels to a plot. This can be done using
the default parameters by setting labelPoints = TRUE in overlay.

Value

no return, plotting side effect

See Also

par, vplot

Examples

require(DESeq2)
simDDS <- DESeq(simDDS)
resAB <- results(simDDS, contrast = c("condition", "A","B"))
resAC <- results(simDDS, contrast = c("condition", "A","C"))
vplot(resAB, xlab = "log2FoldChange", ylab = "-log10(pvalue)")
overlay(resAC, col=2)

harrig12/pointszr documentation built on April 10, 2020, 10:45 p.m.