limma (version 3.28.14)

volcanoplot: Volcano Plot

Description

Creates a volcano plot of log-fold changes versus log-odds of differential expression.

Usage

volcanoplot(fit, coef=1, highlight=0, names=fit$genes$ID, xlab="Log Fold Change", ylab="Log Odds", pch=16, cex=0.35, ...)

Arguments

fit

an MArrayLM fitted linear model object

coef

integer giving the coefficient

highlight

number of top genes to be highlighted

names

character vector giving text labels for the probes to be used in highlighting

xlab

character string giving label for x-axis

ylab

character string giving label for y-axis

pch

vector or list of plotting characters. Default is integer code 16 which gives a solid circle.

cex

numeric vector of plot symbol expansions. Default is 0.35.

...

any other arguments are passed to plot

Value

Details

A volcano plot is any plot which displays fold changes versus a measure of statistical significance of the change.

See Also

An overview of presentation plots following the fitting of a linear model in LIMMA is given in 06.LinearModels.

Examples

#  See lmFit examples