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]