volcanoplot: Volcano Plot

In richierocks/limma2: Linear Models for Microarray Data

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

Details

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

Value

A plot is created on the current graphics device.

Author(s)

Gordon Smyth

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

richierocks/limma2 documentation built on May 27, 2019, 8:47 a.m.