DESeq (version 1.24.0)

plotDispEsts: 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.

Value

The function is called for its side effect.

Details

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

Examples

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