plotSCEBarAssayData: Bar plot of assay data.

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

Bar plot of assay data.

Description

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

Usage

plotSCEBarAssayData(
  inSCE,
  feature,
  sample = NULL,
  useAssay = "counts",
  featureLocation = NULL,
  featureDisplay = NULL,
  groupBy = NULL,
  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.
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.
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 assay data.

Examples

data("mouseBrainSubsetSCE")
plotSCEBarAssayData(
  inSCE = mouseBrainSubsetSCE,
  feature = "Apoe", groupBy = "sex"
)

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