Plot dispersion estimates

Usage

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 2022-03-07.

Author

Michael Steinbaugh

Examples

data(bcb)

## bcbioRNASeq ====
plotDispEsts(bcb)
#> 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"
)
#> estimating size factors
#> estimating dispersions
#> gene-wise dispersion estimates
#> mean-dispersion relationship
#> final dispersion estimates
#> fitting model and testing