plotSCEViolinAssayData: Violin plot of assay data.

Description Usage Arguments Value Examples

View source: R/ggPlotting.R

Description

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

Usage

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plotSCEViolinAssayData(
  inSCE,
  sample = NULL,
  useAssay = "counts",
  feature,
  groupBy = NULL,
  violin = TRUE,
  boxplot = TRUE,
  dots = TRUE,
  xlab = NULL,
  ylab = NULL,
  axisSize = 10,
  axisLabelSize = 10,
  dotSize = 1,
  transparency = 1,
  defaultTheme = TRUE,
  gridLine = FALSE,
  summary = NULL,
  title = NULL,
  titleSize = NULL,
  combinePlot = "none",
  plotLabels = NULL
)

Arguments

inSCE

Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results. Required.

sample

Character vector. Indicates which sample each cell belongs to.

useAssay

Indicate which assay to use. Default "counts".

feature

Name of feature stored in assay of SingleCellExperiment object.

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.

violin

Boolean. If TRUE, will plot the violin plot. Default TRUE.

boxplot

Boolean. If TRUE, will plot boxplots for each violin plot. Default TRUE.

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 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

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 violin plot of assay data.

Examples

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plotSCEViolinAssayData(
  inSCE = mouseBrainSubsetSCE,
  feature = "Apoe", groupBy = "sex"
)

singleCellTK documentation built on Nov. 8, 2020, 5:21 p.m.