A plotting function which visualizes outputs from the runEmptyDrops function stored in the colData slot of the SingleCellExperiment object via scatterplot.
plotEmptyDropsScatter( inSCE, sample = NULL, fdrCutoff = 0.01, defaultTheme = TRUE, dotSize = 0.5, title = NULL, titleSize = 18, xlab = NULL, ylab = NULL, axisSize = 12, axisLabelSize = 15, legendTitle = NULL, legendTitleSize = 12, legendSize = 10, combinePlot = "none", 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 runEmptyDrops. Required. |
---|---|
sample | Character vector. Indicates which sample each cell belongs to. Default NULL. |
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. |
title | Title of plot. Default NULL. |
titleSize | Size of title of plot. Default 18. |
xlab | Character vector. Label for x-axis. Default NULL. |
ylab | Character vector. Label for y-axis. Default NULL. |
axisSize | Size of x/y-axis ticks. Default 12. |
axisLabelSize | Size of x/y-axis labels. Default 15. |
legendTitle | Title of legend. Default NULL. |
legendTitleSize | size of legend title. Default 12. |
legendSize | size of legend. Default 10. |
combinePlot | Boolean. If multiple plots are generated (multiple samples, etc.), will combined plots using `cowplot::plot_grid`. Default TRUE. |
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. |
a ggplot object of the scatter plot.
#>plotEmptyDropsScatter(inSCE=sce)