Plot row standard deviations vs. row means

Usage

plotMeanSd(object, ...)

# S4 method for 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.

Value

ggplot.

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.

Note

Requires the vsn package to be installed.

Updated 2022-10-24.

Author

Michael Steinbaugh, Lorena Patano

Examples

data(bcb)

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