plotBaseMean: Plot base mean distribution

In steinbaugh/DESeqAnalysis: DESeq2 Analysis Utilities

Description

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

Usage

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

• plotBaseMean,DESeqDataSet-method: Generates row means of normalized counts. This value corresponds to the baseMean column of DESeqResults. Passes to numeric method.

• plotBaseMean,DESeqResults-method: Uses baseMean column of results. Passes to numeric method.

• plotBaseMean,DESeqAnalysis-method: Passes to DESeqDataSet method.

Note

Updated 2020-08-04.

See Also

• https://support.bioconductor.org/p/75244/

• summary()

Examples

data(deseq)

## DESeqAnalysis ====
plotBaseMean(deseq)

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