volcanoplot: Volcano Plot

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/plots-fit.R

Description

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

Usage

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volcanoplot(fit, coef = 1, style = "p-value", highlight = 0, names = fit$genes$ID, hl.col="blue",
            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 of length nrow(fit) giving gene names. Only used if highlight > 0.

hl.col

color for the gene names. Only used if highlight > 0.

xlab

character string giving label for x-axis

ylab

character string giving label for y-axis

pch

vector or list of plotting characters.

cex

numeric vector of plot symbol expansions.

...

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

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#  See lmFit examples

hdeberg/limma documentation built on Dec. 20, 2021, 3:43 p.m.