plotEmptyDropsResults {singleCellTK} | R Documentation |
A wrapper function which visualizes outputs from the runEmptyDrops function stored in the colData slot of the SingleCellExperiment object via plots.
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
data(scExample, package="singleCellTK") sce <- runEmptyDrops(inSCE=sce) plotEmptyDropsResults(inSCE=sce)