Visualizes values stored in the colData slot of a SingleCellExperiment object via a bar plot.
plotSCEBarColData(
inSCE,
coldata,
sample = NULL,
groupBy = NULL,
dots = TRUE,
xlab = NULL,
ylab = NULL,
axisSize = 10,
axisLabelSize = 10,
dotSize = 0.1,
transparency = 1,
defaultTheme = TRUE,
gridLine = FALSE,
summary = NULL,
title = NULL,
titleSize = NULL,
combinePlot = TRUE
)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.
- dots
Boolean. If TRUE, will plot dots for each violin plot. Default TRUE.
- 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 10.
- axisLabelSize
Size of x/y-axis labels. Default 10.
- dotSize
Size of dots. Default 0.1.
- transparency
Transparency of the dots, values will be 0-1. Default 1.
- defaultTheme
Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE.
- gridLine
Adds a horizontal grid line if TRUE. Will still be drawn even if defaultTheme is TRUE. Default FALSE.
- summary
Adds a summary statistic, as well as a crossbar to the violin plot. Options are "mean" or "median". Default NULL.
- title
Title of plot. Default NULL.
- titleSize
Size of title of plot. Default 15.
- combinePlot
Boolean. If multiple plots are generated (multiple samples, etc.), will combined plots using `cowplot::plot_grid`. Default TRUE.
Value
a ggplot of the barplot of coldata.
Examples
data("mouseBrainSubsetSCE")
plotSCEBarColData(
inSCE = mouseBrainSubsetSCE,
coldata = "age", groupBy = "sex"
)
