Description Usage Arguments Value Examples
View source: R/ggPerQCWrapper.R
A wrapper function which visualizes outputs from the runEmptyDrops function stored in the colData slot of the SingleCellExperiment object via plots.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | plotEmptyDropsResults(
inSCE,
sample = NULL,
combinePlot = "all",
fdrCutoff = 0.01,
defaultTheme = TRUE,
dotSize = 1,
titleSize = 18,
axisLabelSize = 18,
axisSize = 15,
legendSize = 15,
legendTitleSize = 16,
relHeights = 1,
relWidths = 1,
samplePerColumn = TRUE,
sampleRelHeights = 1,
sampleRelWidths = 1
)
|
inSCE |
Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results from runScrublet. Required. |
sample |
Character vector. Indicates which sample each cell belongs to. 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". |
fdrCutoff |
Numeric. Thresholds barcodes based on the FDR values from runEmptyDrops as "Empty Droplet" or "Putative Cell". Default 0.01. |
defaultTheme |
Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE. |
dotSize |
Size of dots. 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. |
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 | data(scExample, package="singleCellTK")
sce <- runEmptyDrops(inSCE=sce)
plotEmptyDropsResults(inSCE=sce)
|
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