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Last data update: 2014.03.03

R: Plot dispersion estimates and fitted values

plotDispEsts

R Documentation

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`.

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, sanders@fs.tum.de

Examples

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

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(DESeq)
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, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, 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, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

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'.
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/DESeq/plotDispEsts.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotDispEsts
> ### Title: Plot dispersion estimates and fitted values
> ### Aliases: plotDispEsts
> 
> ### ** Examples
> 
> cds <- makeExampleCountDataSet()
> cds <- estimateSizeFactors( cds )
> cds <- estimateDispersions( cds )
> plotDispEsts(cds)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>