Plot total read counts

plotTotalCounts(object, ...)

# S4 method for SummarizedExperiment
plotTotalCounts(object, assay = 1L,
  interestingGroups = NULL, perMillion = FALSE, fill = getOption(x =
  "acid.fill.discrete", default = acidplots::scale_fill_synesthesia_d()),
  labels = list(title = "Total counts", subtitle = NULL, x = NULL, y =
  "counts"), flip = getOption(x = "acid.flip", default = TRUE))

# S4 method for SingleCellExperiment
plotTotalCounts(object, ...)

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.

perMillion

logical(1). Display as counts per million.

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.

flip

logical(1). Flip x and y axes. Recommended for plots containing many samples.

...

Additional arguments.

Value

ggplot.

Methods (by class)

  • SingleCellExperiment: Applies aggregateCellsToSamples() calculation to summarize at sample level prior to plotting.
    Passes ... to SummarizedExperiment method.

Note

Updated 2019-09-16.

Examples

data( RangedSummarizedExperiment, SingleCellExperiment, package = "acidtest" ) ## SummarizedExperiment ==== object <- RangedSummarizedExperiment plotTotalCounts(object)
## SingleCellExperiment ==== object <- SingleCellExperiment plotTotalCounts(object)
#> Aggregating counts using 'sum()'.