Plots for runEmptyDrops outputs.

Source: R/ggPlotting.R

A plotting function which visualizes outputs from the runEmptyDrops function stored in the colData slot of the SingleCellExperiment object via scatter plots.

plotEmptyDropsScatter(
  inSCE,
  sample = NULL,
  fdrCutoff = 0.01,
  defaultTheme = TRUE,
  dotSize = 0.1,
  title = NULL,
  titleSize = 18,
  xlab = NULL,
  ylab = NULL,
  axisSize = 12,
  axisLabelSize = 15,
  legendTitle = NULL,
  legendTitleSize = 12,
  legendSize = 10,
  combinePlot = "none",
  relHeights = 1,
  relWidths = 1,
  samplePerColumn = TRUE,
  sampleRelHeights = 1,
  sampleRelWidths = 1
)

Arguments

inSCE

Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results from runEmptyDrops. Required.

sample

Character vector or colData variable name. Indicates which sample each cell belongs to. Default NULL.

fdrCutoff

Numeric. Thresholds barcodes based on the FDR values from runEmptyDrops as "Empty Droplet" or "Putative Cell". Default 0.01.

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.

legendTitle

Title of legend. Default NULL.

legendTitleSize

size of legend title. Default 12.

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".

relHeights

Relative heights of plots when combine is set. Default 1.

relWidths

Relative widths of plots when combine is set. Default 1.

samplePerColumn

If TRUE, when there are multiple samples and combining by "all", the output .ggplot will have plots from each sample on a single column. Default TRUE.

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 <- runEmptyDrops(inSCE = sce)
#> Sat Mar 18 10:29:16 2023 ... Running 'emptyDrops'
plotEmptyDropsScatter(inSCE = sce)