Plot percentage of zeros vs. library depth

plotZerosVsDepth(object, ...)

# S4 method for SummarizedExperiment
plotZerosVsDepth(object, assay = 1L,
  interestingGroups = NULL, color = getOption(x =
  "acid.color.discrete", default =
  acidplots::scale_colour_synesthesia_d()), title = "Zeros vs. depth")

Arguments

object

Object.

assay

vector(1). Name or index of count matrix slotted in assays(). When passing in a string, the name must be defined in assayNames().

interestingGroups

character. Groups of interest that define the samples. If left unset, defaults to sampleName.

color

ScaleDiscrete. Desired ggplot2 color scale. Must supply discrete values. When set NULL, the default ggplot2 color palette will be used. If manual color definitions are desired, we recommend using ggplot2::scale_color_manual().

To set the discrete color palette globally, use:

options(acid.color.discrete = ggplot2::scale_color_viridis_d())
title

character(1). Plot title.

...

Additional arguments.

Value

ggplot.

Examples

data(sce, package = "acidtest") plotZerosVsDepth(sce)