plotZerosVsDepth: Plot percentage of zeros vs. library depth

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

Plot percentage of zeros vs. library depth

Description

Plot percentage of zeros vs. library depth

Usage

plotZerosVsDepth(object, ...)

## S4 method for signature '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)

acidgenomics/r-acidplots documentation built on April 13, 2025, 11:03 p.m.