plotTotalCounts: Plot total read counts

In acidgenomics/r-acidplots: Acid Genomics Plot Functions and Themes

Plot total read counts

Description

Plot total read counts

Usage

plotTotalCounts(object, ...)

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

## S4 method for signature '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)

acidgenomics/r-acidplots documentation built on March 30, 2024, 10:16 p.m.