plotSCEDensityAssayData: Density plot of assay data.

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Density plot of assay data.

Description

Visualizes values stored in the assay slot of a SingleCellExperiment object via a density plot.

Usage

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
)

Arguments

inSCE	Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results. Required.
feature	Name of feature stored in assay of SingleCellExperiment object.
sample	Character vector. Indicates which sample each cell belongs to.
useAssay	Indicate which assay to use. Default "counts".
featureLocation	Indicates which column name of rowData to query gene.
featureDisplay	Indicates which column name of rowData to use to display feature for visualization.
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.
cutoff	Numeric value. The plot will be annotated with a vertical line if set. 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.

Value

a ggplot of the density plot of assay data.

Examples

data("mouseBrainSubsetSCE")
plotSCEDensityAssayData(
  inSCE = mouseBrainSubsetSCE,
  feature = "Apoe"
)

compbiomed/singleCellTK documentation built on Oct. 27, 2024, 3:26 a.m.