.ggViolin {singleCellTK}R Documentation

Violin plot plotting tool.

Description

Visualizes specified values via a violin plot.

Usage

.ggViolin(
  y,
  groupBy = NULL,
  violin = TRUE,
  boxplot = TRUE,
  dots = TRUE,
  xlab = NULL,
  ylab = NULL,
  baseSize = 12,
  axisSize = NULL,
  axisLabelSize = NULL,
  dotSize = 1,
  transparency = 1,
  defaultTheme = TRUE,
  gridLine = FALSE,
  summary = NULL,
  summaryTextSize = 3,
  combinePlot = "none",
  title = NULL,
  titleSize = NULL
)

Arguments

y

Numeric values to be plotted on y-axis.

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.

baseSize

The base font size for all text. Default 12. Can be overwritten by titleSize, axisSize, and axisLabelSize.

axisSize

Size of x/y-axis ticks. Default NULL.

axisLabelSize

Size of x/y-axis labels. Default NULL.

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.

summaryTextSize

The text size of the summary statistic displayed above the violin plot. Default 3.

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".

title

Title of plot. Default NULL.

titleSize

Size of title of plot. Default 15.

Value

a ggplot of the reduced dimensions.


[Package singleCellTK version 2.2.0 Index]