Plots for runBcds outputs.

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

plotBcdsResults(
  inSCE,
  sample = NULL,
  shape = NULL,
  groupBy = NULL,
  combinePlot = "all",
  violin = TRUE,
  boxplot = FALSE,
  dots = TRUE,
  reducedDimName = "UMAP",
  xlab = NULL,
  ylab = NULL,
  dim1 = NULL,
  dim2 = NULL,
  bin = NULL,
  binLabel = NULL,
  defaultTheme = TRUE,
  dotSize = 0.5,
  summary = "median",
  summaryTextSize = 3,
  transparency = 1,
  baseSize = 15,
  titleSize = NULL,
  axisLabelSize = NULL,
  axisSize = NULL,
  legendSize = NULL,
  legendTitleSize = NULL,
  relHeights = 1,
  relWidths = c(1, 1, 1),
  plotNCols = NULL,
  plotNRows = NULL,
  labelSamples = TRUE,
  samplePerColumn = TRUE,
  sampleRelHeights = 1,
  sampleRelWidths = 1
)

Arguments

inSCE: Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results from runBcds. Required.
sample: Character vector or colData variable name. Indicates which sample each cell belongs to. Default NULL.
shape: If provided, add shapes based on the value. Default NULL.
groupBy: Groupings for each numeric value. A user may input a vector equal length to the number of the samples in inSCE, 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 TRUE.
dots: Boolean. If TRUE, will plot dots for each violin plot. Default TRUE.
reducedDimName: Saved dimension reduction name in inSCE. Default "UMAP".
xlab: Character vector. Label for x-axis. Default NULL.
ylab: Character vector. Label for y-axis. Default NULL.
dim1: 1st dimension to be used for plotting. Can either be a string which specifies the name of the dimension to be plotted from reducedDims, or a numeric value which specifies the index of the dimension to be plotted. Default is NULL.
dim2: 2nd dimension to be used for plotting. Similar to dim1. Default is NULL.
bin: Numeric vector. If single value, will divide the numeric values into bin groups. If more than one value, will bin numeric values using values as a cut point. Default NULL.
binLabel: Character vector. Labels for the bins created by bin. Default NULL.
defaultTheme: Removes grid in plot and sets axis title size to 10 when TRUE. 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 NULL.
summaryTextSize: The text size of the summary statistic displayed above the violin plot. Default 3.
transparency: Transparency of the dots, values will be 0-1. Default 1.
baseSize: The base font size for all text. Default 12. Can be overwritten by titleSize, axisSize, and axisLabelSize, legendSize, legendTitleSize.
titleSize: Size of title of plot. Default NULL.
axisLabelSize: Size of x/y-axis labels. Default NULL.
axisSize: Size of x/y-axis ticks. Default NULL.
legendSize: size of legend. Default NULL.
legendTitleSize: size of legend title. Default NULL.
relHeights: Relative heights of plots when combine is set. Default 1.
relWidths: Relative widths of plots when combine is set. Default c(1, 1, 1).
plotNCols: Number of columns when plots are combined in a grid. Default NULL.
plotNRows: Number of rows when plots are combined in a grid. Default NULL.
labelSamples: Will label sample name in title of plot if TRUE. Default TRUE.
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

list of .ggplot objects

Examples

data(scExample, package="singleCellTK")
sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
sce <- runQuickUMAP(sce)
#> Sat Mar 18 10:28:28 2023 ... Computing Scater UMAP for sample 'pbmc_4k'.
sce <- runBcds(sce)
#> Sat Mar 18 10:28:30 2023 ... Running 'bcds'
plotBcdsResults(inSCE=sce, reducedDimName="UMAP")

Arguments

Value

See also

Examples