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 = 0.5,
titleSize = 18,
axisLabelSize = 18,
axisSize = 15,
legendSize = 15,
legendTitleSize = 16,
relHeights = 1,
relWidths = 1,
samplePerColumn = TRUE,
sampleRelHeights = 1,
sampleRelWidths = 1
)
Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results from runScrublet. Required.
Character vector. Indicates which sample each cell belongs to. 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".
Numeric. Thresholds barcodes based on the FDR values from runEmptyDrops as "Empty Droplet" or "Putative Cell". Default 0.01.
Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE.
Size of dots. Default 0.5.
Size of title of plot. Default 18.
Size of x/y-axis labels. Default 18.
Size of x/y-axis ticks. Default 15.
size of legend. Default 15.
size of legend title. Default 16.
Relative heights of plots when combine is set.
Relative widths of plots when combine is set.
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")
sce <- runEmptyDrops(inSCE=sce)
#> Thu Apr 28 11:26:06 2022 ... Running 'emptyDrops'
plotEmptyDropsResults(inSCE=sce)
#> $scatterEmptyDrops
#>