volcanoplot-methods {xps}R Documentation

Volcano Plot

Description

Produce a scatter plot of fold-change values vs p-values, called volcano plot.

Usage

volcanoplot(x, labels = "", p.value = "pval", mask = FALSE, show.cutoff = TRUE, cex.text = 0.7, col.text = "blue", col.cutoff = "grey", xlim = NULL, xlab = "Log2(Fold-Change)", ylab = "-Log10(P-Value)", pch = '.', ...)

Arguments

x object of class AnalysisTreeSet.
labels optional transcript labels to be drawn at plotting points.
p.value type of p-value, 'pval' for p-value, 'padj' for adjusted p-value, or 'pcha' for p-chance.
mask logical, if TRUE draw only points for transcripts satisfying the univariate test.
show.cutoff logical, if TRUE draw lines indicating cutoff.
cex.text magnification to be used for optional labels.
col.text color to be used for optional labels.
col.cutoff color to be used for lines indicating cutoff, if show.cutoff=TRUE.
xlim optional range for the plotted fold-change values.
xlab label of x-axis.
ylab label of y-axis.
pch either an integer specifying a symbol or a single character to be used as the default in plotting points.
... optional arguments to be passed to plot.

Details

Produces a volcano plot for slot data for an object of class AnalysisTreeSet.

It is possible to label the points of the volcano plot, whereby the following labels parameters are valid:
fUnitName: unit name (probeset ID).
fName: gene name.
fSymbol: gene symbol.
fChromosome: chromosome.
fCytoBand: cytoband.

Author(s)

Christian Stratowa


[Package xps version 1.2.10 Index]