Plots for runPerCellQC outputs.

A wrapper function which visualizes outputs from the runPerCellQC function stored in the colData slot of the SingleCellExperiment object via various plots.

plotRunPerCellQCResults(
  inSCE,
  sample = NULL,
  groupBy = NULL,
  combinePlot = "all",
  violin = TRUE,
  boxplot = FALSE,
  dots = TRUE,
  dotSize = 0.5,
  summary = "median",
  summaryTextSize = 3,
  baseSize = 15,
  axisSize = NULL,
  axisLabelSize = NULL,
  transparency = 1,
  defaultTheme = TRUE,
  titleSize = NULL,
  relHeights = 1,
  relWidths = 1,
  labelSamples = TRUE,
  plotNCols = NULL,
  plotNRows = NULL,
  samplePerColumn = TRUE,
  sampleRelHeights = 1,
  sampleRelWidths = 1
)

Arguments

inSCE	Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results from runPerCellQC. Required.
sample	Character vector. Indicates which sample each cell belongs to. Default NULL.
groupBy	Groupings for each numeric value. A user may input a vector equal length to the number of the samples in the SingleCellExperiment object, or can be retrieved from the colData slot. Default NULL.
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".
violin	Boolean. If TRUE, will plot the violin plot. Default TRUE.
boxplot	Boolean. If TRUE, will plot boxplots for each violin plot. Default FALSE.
dots	Boolean. If TRUE, will plot dots for each violin plot. Default TRUE.
dotSize	Size of dots. Default 0.5.
summary	Adds a summary statistic, as well as a crossbar to the violin plot. Options are "mean" or "median". Default "median".
summaryTextSize	The text size of the summary statistic displayed above the violin plot. Default 3.
baseSize	The base font size for all text. Default 15. Can be overwritten by titleSize, axisSize, and axisLabelSize.
axisSize	Size of x/y-axis ticks. Default NULL.
axisLabelSize	Size of x/y-axis labels. Default NULL.
transparency	Transparency of the dots, values will be 0-1. Default 1.
defaultTheme	Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE.
titleSize	Size of title of plot. Default NULL.
relHeights	Relative heights of plots when combine is set.
relWidths	Relative widths of plots when combine is set.
labelSamples	Will label sample name in title of plot if TRUE. Default TRUE.
plotNCols	Number of columns when plots are combined in a grid.
plotNRows	Number of rows when plots are combined in a grid.
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.
sampleRelWidths	If there are multiple samples and combining by "all", the relative widths for each plot.

Value

list of .ggplot objects

Examples

data(scExample, package="singleCellTK")
if (FALSE) {
sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
sce <- runPerCellQC(sce)
plotRunPerCellQCResults(inSCE=sce)
}