plotBaseMean: Plot base mean distribution

Description Usage Arguments Value Functions Note See Also Examples

Description

The base mean is the mean of normalized counts of all samples, normalizing for sequencing depth.

Usage

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plotBaseMean(object, ...)

## S4 method for signature 'numeric'
plotBaseMean(
  object,
  nonzero = TRUE,
  trans = c("log10", "log2", "identity"),
  summary = TRUE,
  color = getOption(x = "acid.color.discrete", default = getOption(x =
    "ggplot2.discrete.colour", default = AcidPlots::scale_color_synesthesia_d())),
  labels = list(title = "Base mean distribution", subtitle = NULL, x =
    "average expression across all samples", y = "density", color = "summary")
)

## S4 method for signature 'DESeqDataSet'
plotBaseMean(object, ...)

## S4 method for signature 'DESeqResults'
plotBaseMean(object, ...)

## S4 method for signature 'DESeqAnalysis'
plotBaseMean(object, ...)

Arguments

object

Object.

nonzero

logical(1). Remove zero-count features (genes).

trans

character(1). Name of the axis scale transformation to apply.

For more information:

help(topic = "scale_x_continuous", package = "ggplot2")
summary

logical(1). Include distribution summary statistics as lines on the plot.

color

ScaleDiscrete. Desired ggplot2 color scale. Must supply discrete values. When set NULL, the default ggplot2 color palette will be used. If manual color definitions are desired, we recommend using ggplot2::scale_color_manual().

To set the discrete color palette globally, use:

options(acid.color.discrete = ggplot2::scale_color_viridis_d())
labels

list. ggplot2 labels. See ggplot2::labs() for details.

...

Additional arguments.

Value

ggplot.

Functions

Note

Updated 2020-08-04.

See Also

Examples

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data(deseq)

## DESeqAnalysis ====
plotBaseMean(deseq)

steinbaugh/DESeqAnalysis documentation built on Oct. 15, 2020, 2:02 a.m.