Plot percentage of zeros vs. library depth

Usage

plotZerosVsDepth(object, ...)

# S4 method for SummarizedExperiment
plotZerosVsDepth(
  object,
  assay = 1L,
  interestingGroups = NULL,
  pointAlpha = getOption(x = "acid.point.alpha", default = 0.9),
  pointSize = getOption(x = "acid.point.size", default = 1L),
  labels = list(title = "Zeros vs. depth", subtitle = NULL, x = "library size (depth)", y
    = "dropout rate")
)

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.
pointAlpha: numeric(1) (0-1). Alpha transparency level.
pointSize: numeric(1). Point size for dots in the plot. In the range of 1-3 is generally recommended.
labels: list. ggplot2 labels. See ggplot2::labs() for details.
...: Additional arguments.

Value

ggplot.

Note

Updated 2022-11-09.

Examples

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

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


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