plotDispEsts: Plot dispersion estimates

plotDispEstsR Documentation

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 July 25, 2024, 11:11 p.m.