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
)
Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results from runPerCellQC. Required.
Character vector. Indicates which sample each cell belongs to. Default NULL.
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.
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".
Boolean. If TRUE, will plot the violin plot. Default TRUE.
Boolean. If TRUE, will plot boxplots for each violin plot. Default FALSE.
Boolean. If TRUE, will plot dots for each violin plot. Default TRUE.
Size of dots. Default 0.5.
Adds a summary statistic, as well as a crossbar to the violin plot. Options are "mean" or "median". Default "median".
The text size of the summary statistic displayed above the violin plot. Default 3.
The base font size for all text. Default 15. Can be overwritten by titleSize, axisSize, and axisLabelSize.
Size of x/y-axis ticks. Default NULL.
Size of x/y-axis labels. Default NULL.
Transparency of the dots, values will be 0-1. Default 1.
Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE.
Size of title of plot. Default NULL.
Relative heights of plots when combine is set.
Relative widths of plots when combine is set.
Will label sample name in title of plot if TRUE. Default TRUE.
Number of columns when plots are combined in a grid.
Number of rows when plots are combined in a grid.
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.
If there are multiple samples and combining by "all", the relative heights for each plot.
If there are multiple samples and combining by "all", the relative widths for each plot.
list of .ggplot objects
data(scExample, package="singleCellTK")
if (FALSE) {
sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
sce <- runPerCellQC(sce)
plotRunPerCellQCResults(inSCE=sce)
}