plotVolcano: Volcano Plot

In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

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.
	fCytoBand:	cytoband.

Author(s)

Christian Stratowa

See Also

volcanoplot

xps documentation built on Nov. 8, 2020, 6 p.m.