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 )
inSCE | Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results from runScrublet. Required. |
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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 0.5. |
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
#>plotEmptyDropsResults(inSCE=sce)#> $scatterEmptyDrops#>