ggOneToOne: A ggplot-based one-to-one dot plot wrapper function

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

A ggplot-based one-to-one dot plot wrapper function

Description

This function is a wrapper around ggplot geom_point to allow for plotting one-to-one sample comparisons in ArchR.

Usage

ggOneToOne(
  x = NULL,
  y = NULL,
  size = 2,
  alpha = 1,
  xlabel = "x",
  ylabel = "y",
  title = "Correlation",
  min = 0.05,
  max = 0.9999,
  nPlot = 100 * 10^3,
  nKernel = 100,
  densityMax = 0.95,
  extend = 0.05,
  baseSize = 6,
  rastr = TRUE,
  pal = paletteContinuous(set = "blueYellow"),
  ...
)

Arguments

x	A numeric vector containing the x-axis values for each point.
y	A numeric vector containing the y-axis values for each point.
size	The numeric size of the points to plot.
alpha	A number indicating the transparency to use for each point. See ggplot2 for more details.
xlabel	The label to plot for the x-axis.
ylabel	The label to plot for the y-axis.
title	The title of the plot.
min	The lower limit of the x and y axes as a numeric quantile between 0 and 1.
max	The upper limit of the x and y axes as a numeric quantile between 0 and 1.
nPlot	The number of points to plot. When this value is less than the total points, the sample function is used to extract random data points to be plotted.
nKernel	The number of grid points in each direction to use when computing the kernel with MASS::kde2d().
densityMax	The quantile that should be represented by the maximum color on the continuous scale designated by pal. Values above densityMax will be thresholded to the maximum color on the color scale.
extend	A numeric value indicating the fraction to extend the x-axis and y-axis beyond the maximum value on either axis. For example, 0.05 will extend the x-axis and y-axis by 5 percent on each end beyond quantile(c(x,y), max) and quantile(c(x,y), min).
baseSize	The base font size (in points) to use in the plot.
rastr	A boolean value that indicates whether the plot should be rasterized. This does not rasterize lines and labels, just the internal portions of the plot.
pal	A custom palette from ArchRPalettes used to display the density of points on the plot.
...	Additional params to be supplied to ggPoint

Examples

# Create Random Data
m <- data.frame(matrix(rnorm(20, 2),ncol=2))

# Plot
p <- ggOneToOne(x = m[,1], y = m[,2])

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

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