plotDispEsts {DESeq}R Documentation

Plot dispersion estimates and fitted values

Description

A simple helper function that plots the per-gene dispersion estimates together with the fitted mean-dispersion relationship.

Usage

plotDispEsts(cds, name=NULL, ymin, linecol="#ff000080",
  xlab = "mean of normalized counts", ylab = "dispersion",
  log = "xy", cex = 0.45, ... )

Arguments

cds

a CountDataSet.

name

this argument, together with cds, is passed on to fitInfo.

ymin

a scalar numeric, indicating the lower limit of the y-axis. The y-axis is plotted on the logarithmic scale. For the purpose of this plot, per-gene dispersion estimates that are below this value (in particular, those that happen to be zero) are shifted up to this value. If missing, the function attempts to guess a reasonable default.

linecol

colour used for the regression line

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)

Simon Anders, sanders@fs.tum.de

Examples

cds <- makeExampleCountDataSet()
cds <- estimateSizeFactors( cds )
cds <- estimateDispersions( cds )
plotDispEsts(cds)

[Package DESeq version 1.36.0 Index]