plotMA {DESeq} | R Documentation

## Makes a so-called "MA-plot"

### Description

A simple helper function that makes a so-called "MA-plot", i.e. a scatter plot of logarithmic fold changes (on the y-axis) versus the mean of normalized counts (on the x-axis).

### Usage

    plotMA(x, ylim,
      col = ifelse(x$padj>=0.1, "gray32", "red3"),
      linecol = "#ff000080",
      xlab = "mean of normalized counts", ylab = expression(log[2]~fold~change),
      log = "x", cex=0.45, ...)

### Arguments

`x` | a `data.frame` with columns `baseMean`, and `log2FoldChange`. In addition, if the argument `col` is left at its default, this `data.frame` also needs to have a column named `padj`.
`linecol` | colour used for the horizontal line at y=0.
`ylim, col, xlab, ylab, log, cex, ...` | arguments that are passed on to `plot.default`.

### Details

This is a trivial helper function. Do not be afraid to edit and modify it to your needs.

### Value

The function is called for its side effect.

### Author(s)

Wolfgang Huber

### Examples

    ## see vignette

[Package DESeq version 1.39.0 Index]