plotDispEsts {DESeq} | 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)

[Package DESeq version 1.39.0 Index]