plotSCEViolin {singleCellTK} | R Documentation |
Visualizes values stored in any slot of a SingleCellExperiment object via a violin plot.
plotSCEViolin( inSCE, slot, feature, annotation, sample = NULL, groupBy = NULL, violin = TRUE, boxplot = TRUE, dots = TRUE, xlab = NULL, ylab = NULL, axisSize = 10, axisLabelSize = 10, dotSize = 1, transparency = 1, defaultTheme = TRUE, gridLine = FALSE, summary = NULL, title = NULL, titleSize = NULL, combinePlot = "none", plotLabels = NULL )
inSCE |
Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results. Required |
slot |
Desired slot of SingleCellExperiment used for plotting. Possible options: "assays", "colData", "metadata" |
feature |
name of feature stored in assay of SingleCellExperiment object. Required. Will be used only if "assays" slot is chosen. Default NULL. |
annotation |
Desired vector within the slot used for plotting. |
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. |
violin |
Boolean. If TRUE, will plot the violin plot. Default TRUE. |
boxplot |
Boolean. If TRUE, will plot boxplots for each violin plot. Default TRUE. |
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 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 |
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. |
a ggplot of the violin plot.
plotSCEViolin( inSCE = mouseBrainSubsetSCE, slot = "assays", annotation = "counts", feature = "Apoe", groupBy = "sex" )