selectColors: Map a distribution to a color scheme
In raim/segmenTools: Tools for Functional Genome Exploration

selectColors

R Documentation

Map a distribution to a color scheme

Description

Returns a list containing colors and breaks, to be used in image plots, and the cut data and colors for each datum. Note that the function is specifically used for color scheme selection in the genomeBrowser project.

Usage

selectColors(
  x,
  mn,
  mx,
  q = 0.1,
  colf = grDevices::gray.colors,
  reverse = FALSE,
  n = 100,
  plot = TRUE,
  xlab = "score",
  xlim,
  heights = c(0.75, 0.25),
  mai = c(0.75, 0.75, 0.1, 0.1),
  ylim,
  legendf,
  ...
)

Arguments

`x`	data vector
`mn`	minimal value to cut data at, if missing `quantile` will be used with parameter `q` or `q[1]`
`mx`	maximal value to cut data at, if missing the quantile `q[2]` or, if only one q is provided, `1-q[1]` will be used
`q`	parameter `probs` for quantile selection of mn/mx data cuts, here a single value or two values; see `mn` and `mx` arguments
`colf`	color map function used to create a color gradient, eg. `gray.colors` or `viridis`
`reverse`	revert color order
`n`	number of colors, first argument to `colf`
`plot`	plot a legend, ie. a histogram of the full data and an `image` of the color scheme below
`xlab`	x-axis label to use in legend plot
`xlim`	optional limits to x-axis
`heights`	relative heights of histogram and image plots
`mai`	`par("mai")` plot parameter for plot margins
`ylim`	y-axis limits for histogram
`legendf`	legend plot function, called after the upper distribution plot, can be used to add a legend
`...`	further arguments to `colf`, e.g. `start` and `end` in `gray.colors`