plotSCEDensityColData: Density plot of colData.

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

Density plot of colData.

Description

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

Usage

plotSCEDensityColData(
  inSCE,
  coldata,
  sample = NULL,
  groupBy = NULL,
  xlab = NULL,
  ylab = NULL,
  baseSize = 12,
  axisSize = NULL,
  axisLabelSize = NULL,
  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.
coldata	colData value that will be plotted.
sample	Character vector. Indicates which sample each cell belongs to.
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.
baseSize	The base font size for all text. Default 12. Can be overwritten by titleSize, axisSize, and axisLabelSize, legendSize, legendTitleSize.
axisSize	Size of x/y-axis ticks. Default NULL.
axisLabelSize	Size of x/y-axis labels. Default NULL.
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 of the density plot of colData.

Examples

data("mouseBrainSubsetSCE")
plotSCEDensityColData(
  inSCE = mouseBrainSubsetSCE,
  coldata = "age", groupBy = "sex"
)

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