plotMeanSd: Plot row standard deviations vs. row means

In hbc/bcbioRnaseq: Bcbio RNA-Seq

Plot row standard deviations vs. row means

Description

Plot row standard deviations vs. row means

Usage

plotMeanSd(object, ...)

## S4 method for signature 'bcbioRNASeq'
plotMeanSd(
  object,
  fill = ggplot2::scale_fill_gradient(low = AcidPlots::lightPalette[["gray"]], high =
    AcidPlots::lightPalette[["purple"]]),
  lineColor = AcidPlots::lightPalette[["orange"]],
  legend = getOption(x = "acid.legend", default = TRUE)
)

Arguments

object	Object.
fill	ggproto/ScaleDiscrete. Desired ggplot2 fill scale. Must supply discrete values. When set to NULL, the default ggplot2 color palette will be used. If manual color definitions are desired, we recommend using ggplot2::scale_fill_manual(). To set the discrete fill palette globally, use: options("acid.fill.discrete" = ggplot2::scale_fill_viridis_d())
lineColor	character(1). Line color.
legend	logical(1). Include plot legend.
...	Additional arguments.

Details

vsn::meanSdPlot() wrapper that plots count transformations on a log2 scale.

• DESeq2 log2: log2 library size factor-adjusted normalized counts.

• DESeq2 rlog: regularized log transformation.

• DESeq2 VST: variance-stabilizing transformation.

• edgeR log2 TMM: log2 trimmed mean of M-values transformation.

Value

ggplot.

Note

Requires the vsn package to be installed.

Updated 2022-10-24.

Author(s)

Michael Steinbaugh, Lorena Patano

See Also

• vsn::meanSdPlot().

• DESeq2::DESeq().

• DESeq2::rlog().

• DESeq2::varianceStabilizingTransformation().

• edgeR::calcNormFactors().

Examples

data(bcb)

## bcbioRNASeq ====
if (requireNamespace("vsn", quietly = TRUE)) {
    plotMeanSd(bcb)
}

hbc/bcbioRnaseq documentation built on Sept. 15, 2024, 9:10 a.m.