Generate Scaled Viridis Color Palette for Rate Parameters

Creates a named color mapping for a set of numeric parameters (e.g., evolutionary rates) using the viridis color palette. Parameters are first sorted in ascending order and normalized to the range [0, 1], then mapped to evenly spaced viridis colors for intuitive visualization.

Usage

generateViridisColorScale(params)

Arguments

params

A named numeric vector of parameter values (e.g., rates). The names will be preserved and used to label the resulting color mapping.

Value

A named list with two elements:

NamedColors

A named character vector of hex color codes, with names corresponding to the input parameter names, ordered by increasing parameter value.

ParamColorMapping

A named numeric vector of the sorted parameter values, maintaining the same order and names as NamedColors.

Details

This function is useful for plotting results where parameters should be visually distinguished based on their magnitude (e.g., rate shifts across a phylogeny). By using the perceptually uniform viridis palette, it avoids misleading color interpretations common with rainbow scales.

See also

viridis::viridis() for details on the color palette.

Examples

if (requireNamespace("viridis", quietly = TRUE)) {
  library(viridis)
  set.seed(1)
  rates <- c(A = 0.1, B = 0.5, C = 0.9)
  color_scale <- generateViridisColorScale(rates)

  # View the color assignments
  color_scale$NamedColors

  # Plot with colors
  barplot(color_scale$ParamColorMapping,
          col = color_scale$NamedColors,
          main = "Rates with Viridis Colors")
}
#> Loading required package: viridisLite