View source: R/ggPerQCWrapper.R
plotScDblFinderResults | R Documentation |
A wrapper function which visualizes outputs from the
runScDblFinder
function stored in the colData slot of the
SingleCellExperiment object via various plots.
plotScDblFinderResults(
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
)
inSCE |
Input SingleCellExperiment object with saved
dimension reduction components or a variable with saved results from
|
sample |
Character vector or colData variable name. Indicates which
sample each cell belongs to. Default |
shape |
If provided, add shapes based on the value. Default |
groupBy |
Groupings for each numeric value. A user may input a vector
equal length to the number of the samples in |
combinePlot |
Must be either |
violin |
Boolean. If |
boxplot |
Boolean. If |
dots |
Boolean. If |
reducedDimName |
Saved dimension reduction name in |
xlab |
Character vector. Label for x-axis. Default |
ylab |
Character vector. Label for y-axis. Default |
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 |
dim2 |
2nd dimension to be used for plotting. Similar to |
bin |
Numeric vector. If single value, will divide the numeric values
into |
binLabel |
Character vector. Labels for the bins created by |
defaultTheme |
Removes grid in plot and sets axis title size to
|
dotSize |
Size of dots. Default |
summary |
Adds a summary statistic, as well as a crossbar to the
violin plot. Options are |
summaryTextSize |
The text size of the summary statistic displayed
above the violin plot. Default |
transparency |
Transparency of the dots, values will be 0-1. Default
|
baseSize |
The base font size for all text. Default |
titleSize |
Size of title of plot. Default |
axisLabelSize |
Size of x/y-axis labels. Default |
axisSize |
Size of x/y-axis ticks. Default |
legendSize |
size of legend. Default |
legendTitleSize |
size of legend title. Default |
relHeights |
Relative heights of plots when combine is set. Default |
relWidths |
Relative widths of plots when combine is set. Default
|
plotNCols |
Number of columns when plots are combined in a grid. Default
|
plotNRows |
Number of rows when plots are combined in a grid. Default
|
labelSamples |
Will label sample name in title of plot if TRUE. Default
|
samplePerColumn |
If |
sampleRelHeights |
If there are multiple samples and combining by
|
sampleRelWidths |
If there are multiple samples and combining by
|
list of .ggplot objects
runScDblFinder
data(scExample, package="singleCellTK")
sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
sce <- runQuickUMAP(sce)
sce <- runScDblFinder(sce)
plotScDblFinderResults(inSCE = sce, reducedDimName = "UMAP")
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