plotSCEBarColData: Bar plot of colData.

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

Bar plot of colData.

Description

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

Usage

plotSCEBarColData(
  inSCE,
  coldata,
  sample = NULL,
  groupBy = NULL,
  dots = TRUE,
  xlab = NULL,
  ylab = NULL,
  axisSize = 10,
  axisLabelSize = 10,
  dotSize = 0.1,
  transparency = 1,
  defaultTheme = TRUE,
  gridLine = FALSE,
  summary = NULL,
  title = NULL,
  titleSize = NULL,
  combinePlot = TRUE
)

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.
dots	Boolean. If TRUE, will plot dots for each violin plot. Default TRUE.
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.
dotSize	Size of dots. Default 0.1.
transparency	Transparency of the dots, values will be 0-1. Default 1.
defaultTheme	Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE.
gridLine	Adds a horizontal grid line if TRUE. Will still be drawn even if defaultTheme is TRUE. Default FALSE.
summary	Adds a summary statistic, as well as a crossbar to the violin plot. Options are "mean" or "median". Default NULL.
title	Title of plot. Default NULL.
titleSize	Size of title of plot. Default 15.
combinePlot	Boolean. If multiple plots are generated (multiple samples, etc.), will combined plots using 'cowplot::plot_grid'. Default TRUE.

Value

a ggplot of the barplot of coldata.

Examples

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

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