xps (version 1.32.0)

plotVolcano: Volcano Plot

Description

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

Usage

plotVolcano(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         = '.', dev         = "screen", outfile     = "VolcanoPlot", w           = 540, h           = 540, ...)

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.

dev

graphics device to plot to, i.e. one of “screen”, “jpeg”,“png”, “pdf” or “ps”.

outfile

the name of the output file.

w

the width of the device in pixels.

h

the height of the device in pixels.

...

optional arguments to be passed to barplot.

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.

See Also

volcanoplot