Plots for runBarcodeRankDrops outputs.

A plotting function which visualizes outputs from the runBarcodeRankDrops function stored in the colData slot of the SingleCellExperiment object via scatterplot.

plotBarcodeRankScatter(
  inSCE,
  sample = NULL,
  defaultTheme = TRUE,
  dotSize = 0.1,
  title = NULL,
  titleSize = 18,
  xlab = NULL,
  ylab = NULL,
  axisSize = 12,
  axisLabelSize = 15,
  legendSize = 10,
  combinePlot = "none",
  sampleRelHeights = 1,
  sampleRelWidths = 1
)

Arguments

inSCE: Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results from runBarcodeRankDrops. Required.
sample: Character vector or colData variable name. Indicates which sample each cell belongs to. Default NULL.
defaultTheme: Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE.
dotSize: Size of dots. Default 0.1.
title: Title of plot. Default NULL.
titleSize: Size of title of plot. Default 18.
xlab: Character vector. Label for x-axis. Default NULL.
ylab: Character vector. Label for y-axis. Default NULL.
axisSize: Size of x/y-axis ticks. Default 12.
axisLabelSize: Size of x/y-axis labels. Default 15.
legendSize: size of legend. Default 10.
combinePlot: Must be either "all", "sample", or "none". "all" will combine all plots into a single .ggplot object, while "sample" will output a list of plots separated by sample. Default "all".
sampleRelHeights: If there are multiple samples and combining by "all", the relative heights for each plot. Default 1.
sampleRelWidths: If there are multiple samples and combining by "all", the relative widths for each plot. Default 1.

Value

a ggplot object of the scatter plot.

Examples

data(scExample, package = "singleCellTK")
sce <- runBarcodeRankDrops(inSCE = sce)
#> Sat Mar 18 10:28:20 2023 ... Running 'barcodeRanks'
plotBarcodeRankScatter(inSCE = sce)
#> Warning: Transformation introduced infinite values in continuous y-axis

Arguments

Value

See also

Examples