Plot counts per biotype

plotCountsPerBiotype(object, ...)

# S4 method for SummarizedExperiment
plotCountsPerBiotype(object, assay = 1L,
  n = 9L, interestingGroups = NULL, trans = c("identity", "log2",
  "log10"), fill = getOption(x = "acid.fill.discrete", default =
  acidplots::scale_fill_synesthesia_d()), countsAxisLabel = "counts",
  title = "Counts per biotype")

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().

n

integer(1). Number to include.

interestingGroups

character. Groups of interest that define the samples. If left unset, defaults to sampleName.

trans

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

For more information:

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

character(1). Counts axis label.

title

character(1). Plot title.

...

Additional arguments.

Value

ggplot.

Examples

data(rse, sce, package = "acidtest") ## SummarizedExperiment ==== plotCountsPerBiotype(rse)
## SingleCellExperiment ==== plotCountsPerBiotype(sce)