Plot genes detected

Plot genes detected

# S4 method for SummarizedExperiment
plotGenesDetected(object, assay = 1L,
  interestingGroups = NULL, limit = 0L, minCounts = 1L,
  fill = getOption("basejump.fill.discrete", NULL),
  flip = getOption("basejump.flip", TRUE), title = "genes detected")

# S4 method for SingleCellExperiment
plotGenesDetected(object, assay = 1L,
  interestingGroups = NULL, limit = 0L, minCounts = 1L,
  fill = getOption("basejump.fill.discrete", NULL),
  flip = getOption("basejump.flip", TRUE), title = "genes detected")

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.
limit	numeric(1). Threshold to denote on the plot, using a dashed line.
minCounts	integer(1). Minimum number of counts per gene in the count matrix.
fill	ggproto/ScaleDiscrete. Desired ggplot2 fill scale. Must supply discrete values. When set to NULL, the default ggplot2 color palette will be used. If manual color definitions are desired, we recommend using ggplot2::scale_fill_manual(). To set the discrete fill palette globally, use: options(basejump.fill.discrete = ggplot2::scale_fill_viridis_d())
flip	logical(1). Flip x and y axes. Recommended for plots containing many samples.
title	character(1). Plot title.

Value

ggplot.

Examples

data(rse, sce)
plotGenesDetected(rse)
plotGenesDetected(sce)
#> Aggregating counts using sum().