Plot total read counts

Usage

plotTotalCounts(object, ...)

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

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

Arguments

object: Object.
...: Additional arguments.
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.
labels: list. ggplot2 labels. See ggplot2::labs() for details.
flip: logical(1). Flip x and y axes. Recommended for plots containing many samples.

Value

ggplot.

Functions

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

Note

Updated 2022-03-04.

Examples

data(
    RangedSummarizedExperiment,
    SingleCellExperiment_splatter,
    package = "AcidTest"
)

## SummarizedExperiment ====
object <- RangedSummarizedExperiment
plotTotalCounts(object)


## SingleCellExperiment ====
object <- SingleCellExperiment_splatter
plotTotalCounts(object)