Plot sexually dimorphic gender marker genes

This is a convenience function that quickly plots known sexually dimorphic genes, and overall gene experssion for the X and Y chromosomes.

# S4 method for SummarizedExperiment
plotGenderMarkers(object, assay = 1L,
  interestingGroups = NULL, countsAxisLabel = "counts",
  medianLine = TRUE, color = getOption("basejump.discrete.color",
  NULL), legend = getOption("basejump.legend", TRUE), style = "wide")

Arguments

object	Object.
assay	vector(1). Name or index of count matrix slotted in assays(). When passing in a string, the name must be defined in assayNames().
interestingGroups	character. Groups of interest that define the samples. If left unset, defaults to sampleName.
countsAxisLabel	character(1). Label to use for the counts axis.
medianLine	logical(1). Include median line for each group. Disabled if samples are colored by sample name.
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(basejump.color.discrete = ggplot2::scale_color_viridis_d())
legend	logical(1). Show plot legend.
style	character(1). Plot style.
...	Additional arguments.

Value

ggplot.

Note

Currently only Homo sapiens and Mus musculus genomes are supported.

See also

plotCounts().