ggHex: A ggplot-based Hexplot wrapper function summary of points in...

In haibol2016/ArchR_debug: Analyzing single-cell regulatory chromatin in R.

A ggplot-based Hexplot wrapper function summary of points in a standardized manner

Description

This function will plot x,y coordinate values summarized in hexagons in a standardized manner

Usage

ggHex(
  x = NULL,
  y = NULL,
  color = NULL,
  pal = paletteContinuous(set = "solarExtra"),
  bins = 200,
  xlim = NULL,
  ylim = NULL,
  extend = 0.05,
  xlabel = "x",
  ylabel = "y",
  title = "",
  colorTitle = "values",
  baseSize = 6,
  ratioYX = 1,
  FUN = "median",
  hexCut = c(0.02, 0.98),
  addPoints = FALSE,
  ...
)

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.
color	A numeric/categorical vector containing coloring information for each point.
pal	A custom continuous palette from ArchRPalettes for coloration of hexes.
bins	The number of bins to be used for plotting the hexplot. bins indicates the total number of hexagons that will fit within the surface area of the plot.
xlim	A numeric vector of two values indicating the lower and upper bounds of the x-axis on the plot.
ylim	A numeric vector of two values indicating the lower and upper bounds of the y-axis on the plot.
extend	A numeric value indicating the fraction to extend the x-axis and y-axis beyond the maximum and minimum values if xlim and ylim are not provided. For example, 0.05 will extend the x-axis and y-axis by 5 percent on each end.
xlabel	The label to plot for the x-axis.
ylabel	The label to plot for the y-axis.
title	The title of the plot.
colorTitle	The label to use for the legend corresponding to color.
baseSize	The base font size (in points) to use in the plot.
ratioYX	The aspect ratio of the x and y axes on the plot.
FUN	The function to use for summarizing data into hexagons. Typically "mean" or something similar.
hexCut	If this is not null, a quantile cut is performed to threshold the top and bottom of the distribution of values. This prevents skewed color scales caused by strong outliers. The format of this should be c(a,b) where a is the upper threshold and b is the lower threshold. For example, hexCut = c(0.025,0.975) will take the top and bottom 2.5 percent of values and set them to the value of the 97.5th and 2.5th percentile values respectively.
addPoints	A boolean value indicating whether individual points should be shown on the hexplot.
...	Additional params for plotting

haibol2016/ArchR_debug documentation built on June 15, 2022, 5:42 p.m.