plotDispEsts: Plot dispersion estimates and fitted values

In DESeq: Differential gene expression analysis based on the negative binomial distribution

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, [e-mail]

Examples

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

Example output

Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: lattice
    Welcome to 'DESeq'. For improved performance, usability and
    functionality, please consider migrating to 'DESeq2'.

DESeq documentation built on April 28, 2020, 6:37 p.m.