Visualizes values stored in the assay slot of a SingleCellExperiment object via a density plot.
plotSCEDensityAssayData(
inSCE,
feature,
sample = NULL,
useAssay = "counts",
featureLocation = NULL,
featureDisplay = NULL,
groupBy = NULL,
xlab = NULL,
ylab = NULL,
axisSize = 10,
axisLabelSize = 10,
defaultTheme = TRUE,
cutoff = NULL,
title = NULL,
titleSize = 18,
combinePlot = "none",
plotLabels = NULL
)
Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results. Required.
Name of feature stored in assay of SingleCellExperiment object.
Character vector. Indicates which sample each cell belongs to.
Indicate which assay to use. Default "counts".
Indicates which column name of rowData to query gene.
Indicates which column name of rowData to use to display feature for visualization.
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.
Character vector. Label for x-axis. Default NULL.
Character vector. Label for y-axis. Default NULL.
Size of x/y-axis ticks. Default 10.
Size of x/y-axis labels. Default 10.
Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE.
Numeric value. The plot will be annotated with a vertical line if set. Default NULL.
Title of plot. Default NULL.
Size of title of plot. Default 15.
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".
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 density plot of assay data.
data("mouseBrainSubsetSCE")
plotSCEDensityAssayData(
inSCE = mouseBrainSubsetSCE,
feature = "Apoe"
)
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