R/ggPlotting.R
plotSCEViolin.Rd
Visualizes values stored in any slot of a SingleCellExperiment object via a violin plot.
plotSCEViolin( inSCE, slotName, itemName, feature = NULL, sample = NULL, dimension = NULL, groupBy = NULL, violin = TRUE, boxplot = TRUE, dots = TRUE, xlab = NULL, ylab = NULL, axisSize = 10, axisLabelSize = 10, dotSize = 0.5, 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. |
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slotName | Desired slot of SingleCellExperiment used for plotting. Possible options: "assays", "colData", "metadata", "reducedDims". Required. |
itemName | Desired vector within the slot used for plotting. Required. |
feature | Desired name of feature stored in assay of SingleCellExperiment object. Only used when "assays" slotName is selected. Default NULL. |
sample | Character vector. Indicates which sample each cell belongs to. |
dimension | Desired dimension stored in the specified reducedDims. Either an integer which indicates the column or a character vector specifies column name. By default, the 1st dimension/column will be used. Only used when "reducedDims" slotName is selected. Default NULL. |
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 0.5. |
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, slotName = "assays", itemName = "counts", feature = "Apoe", groupBy = "sex" )