ArchR_debug: Analyzing single-cell regulatory chromatin in R.

ggGroup

R Documentation

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.