plotSCEDensity {singleCellTK} | R Documentation |
Visualizes values stored in any slot of a SingleCellExperiment object via a densityn plot.
plotSCEDensity( inSCE, slotName, itemName, sample = NULL, feature = NULL, dimension = NULL, groupBy = NULL, xlab = NULL, ylab = NULL, axisSize = 10, axisLabelSize = 10, defaultTheme = TRUE, title = NULL, titleSize = 18, cutoff = NULL, combinePlot = "none", plotLabels = NULL )
inSCE |
Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results. Required. |
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. |
sample |
Character vector. Indicates which sample each cell belongs to. |
feature |
Desired name of feature stored in assay of SingleCellExperiment object. Only used when "assays" slotName is selected. Default NULL. |
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. |
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. |
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. |
a ggplot object of the density plot.
plotSCEDensity( inSCE = mouseBrainSubsetSCE, slotName = "assays", itemName = "counts", feature = "Apoe", groupBy = "sex" )