Visualizes values stored in the colData slot of a SingleCellExperiment object via a density plot.
plotSCEDensityColData(
inSCE,
coldata,
sample = NULL,
groupBy = NULL,
xlab = NULL,
ylab = NULL,
baseSize = 12,
axisSize = NULL,
axisLabelSize = NULL,
defaultTheme = TRUE,
title = NULL,
titleSize = 18,
cutoff = NULL,
combinePlot = "none",
plotLabels = NULL
)Arguments
- inSCE
Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results. Required.
- coldata
colData value that will be plotted.
- sample
Character vector. Indicates which sample each cell belongs to.
- groupBy
Groupings for each numeric value. A user may input a vector equal length to the number of the samples in the SingleCellExperiment object, or can be retrieved from the colData slot. Default NULL.
- xlab
Character vector. Label for x-axis. Default NULL.
- ylab
Character vector. Label for y-axis. Default NULL.
- baseSize
The base font size for all text. Default 12. Can be overwritten by titleSize, axisSize, and axisLabelSize, legendSize, legendTitleSize.
- axisSize
Size of x/y-axis ticks. Default NULL.
- axisLabelSize
Size of x/y-axis labels. Default NULL.
- defaultTheme
Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE.
- title
Title of plot. Default NULL.
- titleSize
Size of title of plot. Default 15.
- cutoff
Numeric value. The plot will be annotated with a vertical line if set. 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 "none".
- plotLabels
labels to each plot. If set to "default", will use the name of the samples as the labels. If set to "none", no label will be plotted.
Value
a ggplot of the density plot of colData.
Examples
data("mouseBrainSubsetSCE")
plotSCEDensityColData(
inSCE = mouseBrainSubsetSCE,
coldata = "age", groupBy = "sex"
)
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