ggGroup: A ggplot-based ridge/violin plot wrapper function

In GreenleafLab/ArchR: Analyzing single-cell regulatory chromatin in R.

A ggplot-based ridge/violin plot wrapper function

Description

This function is a wrapper around ggplot geom_density_ridges or geom_violin to allow for plotting group distribution plots in ArchR.

Usage

ggGroup(
  x = NULL,
  y = NULL,
  xlabel = NULL,
  ylabel = NULL,
  groupOrder = NULL,
  groupSort = FALSE,
  size = 1,
  baseSize = 10,
  ridgeScale = 1,
  ratioYX = NULL,
  alpha = 1,
  title = "",
  pal = paletteDiscrete(values = x, set = "stallion"),
  addBoxPlot = TRUE,
  plotAs = "ridges",
  ...
)

Arguments

x	A character vector containing the categorical x-axis values for each y-axis value.
y	A numeric vector containing the y-axis values for each point.
xlabel	The label to plot for the x-axis.
ylabel	The label to plot for the y-axis.
groupOrder	A character vector indicating a custom order for plotting x-axis categorical values. Should contain all possible values of x in the desired order.
groupSort	A boolean indicating whether to sort groups based on the average value of the group.
size	The line width for boxplot/summary lines.
baseSize	The base font size (in points) to use in the plot.
ridgeScale	A numeric indicating the relative size for each ridge in the ridgeplot.
ratioYX	The aspect ratio of the x and y axes on the plot.
alpha	A number indicating the transparency to use for each point. See ggplot2 for more details.
title	The title of the plot.
pal	A named custom palette (see paletteDiscrete() and ArchRPalettes) for discrete coloring.
addBoxPlot	A boolean indicating whether to add a boxplot to the plot if plotAs="violin".
plotAs	A string indicating how the groups should be plotted. Acceptable values are "ridges" (for a ggrides-style plot) or "violin" (for a violin plot).
...	Additional parameters to pass to ggplot2 for plotting.

Examples

# Create Random Data
m <- data.frame(x=matrix(rnorm(10, 2),ncol=1))
m$color <- sample(c("A", "B"), 10, replace = TRUE)

# Plot
p <- ggGroup(x = m$color, y = m$x)

# To PDF
pdf("test.pdf", width = 4, height = 4)
p
dev.off()

GreenleafLab/ArchR documentation built on Feb. 21, 2025, 3:05 p.m.