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