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

Description Usage Arguments

Description

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

Usage

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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


RyanYip-Kat/yipCat documentation built on Dec. 18, 2021, 11:55 a.m.