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
)
Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results from runEmptyDrops. Required.
Character vector. Indicates which sample each cell belongs to. Default NULL.
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.
Title of plot. Default NULL.
Size of title of plot. Default 18.
Character vector. Label for x-axis. Default NULL.
Character vector. Label for y-axis. Default NULL.
Size of x/y-axis ticks. Default 12.
Size of x/y-axis labels. Default 15.
Title of legend. Default NULL.
size of legend title. Default 12.
size of legend. Default 10.
Boolean. If multiple plots are generated (multiple samples, etc.), will combined plots using `cowplot::plot_grid`. Default TRUE.
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.
a ggplot object of the scatter plot.
data(scExample, package="singleCellTK")
sce <- runEmptyDrops(inSCE=sce)
#> Thu Apr 28 11:26:16 2022 ... Running 'emptyDrops'
plotEmptyDropsScatter(inSCE=sce)