Plot cell counts

plotCellCounts(object, ...)

# S4 method for SingleCellExperiment
plotCellCounts(
  object,
  interestingGroups = NULL,
  fill = getOption(x = "acid.fill.discrete", default = getOption(x =
    "ggplot2.discrete.fill", default = AcidPlots::scale_fill_synesthesia_d())),
  labels = list(title = "Cell counts", subtitle = NULL, x = NULL, y = "cells")
)

Arguments

object

Object.

interestingGroups

character. Groups of interest to use for visualization. Corresponds to factors describing the columns of the 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())
labels

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

...

Additional arguments.

Value

ggplot.

Note

Updated 2019-12-09.

Author

Michael Steinbaugh, Rory Kirchner

Examples

data(SingleCellExperiment, package = "AcidTest") ## SingleCellExperiment ==== object <- SingleCellExperiment plotCellCounts(object)