Plot counts per broad class definition

plotCountsPerBroadClass(object, ...)

# S4 method for SummarizedExperiment
plotCountsPerBroadClass(object,
  assay = 1L, interestingGroups = NULL, trans = c("identity", "log2",
  "log10"), fill = getOption(x = "acid.fill.discrete", default =
  acidplots::scale_fill_synesthesia_d()), labels = list(title =
  "Counts per broad class", subtitle = NULL, sampleAxis = NULL, countAxis =
  "counts"))

Arguments

object

Object.

assay

vector(1). Assay name or index position.

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

Plot.

Note

Updated 2019-09-16.

Examples

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