Plot dispersion estimates

A simple helper function that plots the per-gene dispersion estimates together with the fitted mean-dispersion relationship.

plotDispEsts(object, ...)

# S4 method for bcbioRNASeq
plotDispEsts(object, ...)

Arguments

object	Object.
...	Passthrough to DESeqDataSet method defined in DESeq2. See DESeq2::plotDispEsts() for details.

Value

ggplot.

Details

This plot shows the dispersion by mean of normalized counts. We expect the dispersion to decrease as the mean of normalized counts increases.

Here we're generating a DESeqDataSet object on the fly, which already has method support for plotting dispersion, provided by the DESeq2 package.

Note

Updated 2019-09-15.

See also

DESeq2::plotDispEsts().

Examples

data(bcb)
plotDispEsts(bcb)
#> Generating DESeqDataSet with DESeq2 1.25.17.
#> estimating size factors
#> estimating dispersions
#> gene-wise dispersion estimates
#> mean-dispersion relationship
#> final dispersion estimates
#> fitting model and testing

## Custom colors, using DESeq2 parameters.
plotDispEsts(
    object = bcb,
    genecol = "gray",
    fitcol = "purple",
    finalcol = "orange"
)
#> Generating DESeqDataSet with DESeq2 1.25.17.
#> estimating size factors
#> estimating dispersions
#> gene-wise dispersion estimates
#> mean-dispersion relationship
#> final dispersion estimates
#> fitting model and testing