Description Usage Arguments Value Examples
View source: R/ggPerQCWrapper.R
A wrapper function which visualizes outputs from the runDoubletCells function stored in the colData slot of the SingleCellExperiment object via various plots.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 | plotDoubletCellsResults(
inSCE,
sample = NULL,
shape = NULL,
groupBy = NULL,
combinePlot = "all",
violin = TRUE,
boxplot = FALSE,
dots = TRUE,
reducedDimName = NULL,
xlab = NULL,
ylab = NULL,
dim1 = NULL,
dim2 = NULL,
bin = NULL,
binLabel = NULL,
defaultTheme = TRUE,
dotSize = 1,
transparency = 1,
titleSize = 18,
axisLabelSize = 18,
axisSize = 15,
legendSize = 15,
legendTitleSize = 16,
relHeights = c(1.5, 1, 1),
relWidths = c(1, 1, 1),
plotNCols = NULL,
plotNRows = NULL,
plotLabels = "default",
plotLabelSize = 20,
plotLabelPositionX = NULL,
plotLabelPositionY = NULL,
samplePerColumn = TRUE,
sampleRelHeights = 1,
sampleRelWidths = 1
)
|
inSCE |
Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results from runDoubletCells. Required. |
sample |
Character vector. Indicates which sample each cell belongs to. Default NULL. |
shape |
If provided, add shapes based on the value. |
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 TRUE. |
dots |
Boolean. If TRUE, will plot dots for each violin plot. Default TRUE. |
reducedDimName |
Saved dimension reduction name in the SingleCellExperiment object. Required. |
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. 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. |
bin |
Numeric vector. If single value, will divide the numeric values into the 'bin' groups. If more than one value, will bin numeric values using values as a cut point. |
binLabel |
Character vector. Labels for the bins created by the 'bin' parameter. Default NULL. |
defaultTheme |
Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE. |
dotSize |
Size of dots. Default 1. |
transparency |
Transparency of the dots, values will be 0-1. Default 1. |
titleSize |
Size of title of plot. Default 18. |
axisLabelSize |
Size of x/y-axis labels. Default 18. |
axisSize |
Size of x/y-axis ticks. Default 15. |
legendSize |
size of legend. Default 15. |
legendTitleSize |
size of legend title. Default 16. |
relHeights |
Relative heights of plots when combine is set. |
relWidths |
Relative widths of plots when combine is set. |
plotNCols |
Number of columns when plots are combined in a grid. |
plotNRows |
Number of rows when plots are combined in a grid. |
plotLabels |
labels to each plot. If set to "default", will use the name of the samples as the labels. If set to "none", no label will be plotted. |
plotLabelSize |
size of labels |
plotLabelPositionX |
Numeric vector. The X position of the plot label. |
plotLabelPositionY |
Numeric vector. The Y position of the plot label. |
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. |
list of .ggplot objects
1 2 3 4 5 | data(scExample, package="singleCellTK")
sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
sce <- getUMAP(inSCE=sce, useAssay="counts", reducedDimName="UMAP")
sce <- runDoubletCells(sce)
plotDoubletCellsResults(inSCE=sce, reducedDimName="UMAP")
|
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