plotEmptyDropsScatter {singleCellTK} | R Documentation |
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 = 1, 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 1. |
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.
data(scExample, package="singleCellTK") sce <- runEmptyDrops(inSCE=sce) plotEmptyDropsScatter(inSCE=sce)