plotDispEsts: Plot dispersion estimates

In mikelove/DESeq2: Differential gene expression analysis based on the negative binomial distribution

Plot dispersion estimates

Description

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

Usage

## S4 method for signature 'DESeqDataSet'
plotDispEsts(
  object,
  ymin,
  CV = FALSE,
  genecol = "black",
  fitcol = "red",
  finalcol = "dodgerblue",
  legend = TRUE,
  xlab,
  ylab,
  log = "xy",
  cex = 0.45,
  ...
)

Arguments

object	a DESeqDataSet, with dispersions estimated
ymin	the lower bound for points on the plot, points beyond this are drawn as triangles at ymin
CV	logical, whether to plot the asymptotic or biological coefficient of variation (the square root of dispersion) on the y-axis. As the mean grows to infinity, the square root of dispersion gives the coefficient of variation for the counts. Default is FALSE, plotting dispersion.
genecol	the color for gene-wise dispersion estimates
fitcol	the color of the fitted estimates
finalcol	the color of the final estimates used for testing
legend	logical, whether to draw a legend
xlab	xlab
ylab	ylab
log	log
cex	cex
...	further arguments to plot

Author(s)

Simon Anders

Examples

dds <- makeExampleDESeqDataSet()
dds <- estimateSizeFactors(dds)
dds <- estimateDispersions(dds)
plotDispEsts(dds)

mikelove/DESeq2 documentation built on Nov. 18, 2024, 1:37 p.m.