DESeq2: plotDispEsts – R documentation

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plotDispEsts

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)

DESeq2

Differential gene expression analysis based on the negative binomial distribution

v1.30.1

LGPL (>= 3)

Authors

Michael Love [aut, cre], Constantin Ahlmann-Eltze [ctb], Kwame Forbes [ctb], Simon Anders [aut, ctb], Wolfgang Huber [aut, ctb]

Initial release