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()), labels = list(title =
  "Counts per biotype", subtitle = NULL, sampleAxis = NULL, countAxis =
  "counts"))

# S4 method for SingleCellExperiment
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()), labels = list(title =
  "Counts per biotype", subtitle = NULL, sampleAxis = NULL, countAxis =
  "counts"))

Arguments

object

Object.

assay

vector(1). Assay name or index position.

n

integer(1). Number to include.

interestingGroups

character. Groups of interest to use for visualization. Corresponds to factors describing the columns of the object.

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())
labels

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

...

Additional arguments.

Value

ggplot.

Note

Updated 2019-09-16.

Examples

data( RangedSummarizedExperiment, SingleCellExperiment, package = "acidtest" ) ## SummarizedExperiment ==== object <- RangedSummarizedExperiment plotCountsPerBiotype(object)
#> 500 / 500 features passed 'perRow' >= 1 cutoff.
## SingleCellExperiment ==== object <- SingleCellExperiment plotCountsPerBiotype(object)
#> 478 / 500 features passed 'perRow' >= 1 cutoff.