volcanoplot {limma} | R Documentation

## Volcano Plot

### Description

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

### Usage

    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

    #  See lmFit examples

[Package limma version 3.38.3 Index]