volcanoplot {limma}R Documentation

Volcano Plot

Description

Creates a volcano plot for a specified coefficient of a linear model.

Usage

volcanoplot(fit, coef = 1L, style = "p-value", highlight = 0, names = fit$genes$ID,
            xlab = "Log2 Fold Change", ylab = NULL, pch=16, cex=0.35, ...)

Arguments

fit

an MArrayLM fitted linear model object.

coef

index indicating which coefficient of the linear model is to be plotted.

style

character string indicating which significance statistic to plot on the y-axis. Possibilities are "p-value" or "B-statistic".

highlight

number of top genes to be highlighted by name.

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 displays log fold changes on the x-axis versus a measure of statistical significance on the y-axis. Here the significance measure can be -log(p-value) or the B-statistics, which give the posterior log-odds of differential expression.

The plot is optionally annotated with the names of the most significant genes.

Value

No value is returned but 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

[Package limma version 3.34.5 Index]