plotSCEDensity: Density plot of any data stored in the SingleCellExperiment...

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

Density plot of any data stored in the SingleCellExperiment object.

Description

Visualizes values stored in any slot of a SingleCellExperiment object via a densityn plot.

Usage

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
)

Arguments

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.

Value

a ggplot object of the density plot.

Examples

data("mouseBrainSubsetSCE")
plotSCEDensity(
  inSCE = mouseBrainSubsetSCE, slotName = "assays",
  itemName = "counts", feature = "Apoe", groupBy = "sex"
)

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