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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)