colors_from_values: Retrieve colors based on numeric values

In TheJacksonLaboratory/cape: Combined Analysis of Pleiotropy and Epistasis for Diversity Outbred Mice

Retrieve colors based on numeric values

Description

This function gets colors for numeric values It can use one the function get_color, which accepts any of c("green", "purple", "orange", "blue", "brown", "gray"), or it can use pheatmap colors. The colors can be split into multiple classes based on split_points. For example positive and negative numbers can each be plotted on their own scale, by setting split_at_vals to TRUE and setting split_points to 0. split_points can be a vector defining multiple value classes for different colors. By default, the different classes use the col_scale colors in order. Specific colors for classes can be set using the col_scale argument.

Usage

colors_from_values(
  vals,
  split_at_vals = FALSE,
  split_points = 0,
  col_scale = c("green", "purple", "orange", "blue", "brown", "gray"),
  light_dark = "f",
  grad_dir = c("high", "low", "middle", "ends"),
  color_fun = c("linear", "exponential"),
  exp_steepness = 1,
  global_color_scale = FALSE,
  global_min = NULL,
  global_max = NULL,
  use_pheatmap_colors = FALSE,
  na_col = "lightgray"
)

Arguments

vals	A vector of numerical values for which to retrieve colors.
split_at_vals	A logical value indicating whether the numbers should be broken into classes with different colors.
split_points	If split_at_vals is TRUE, split_points is used to define multiple classes of numbers. For example, if split_points is 0, negative numbers will be assigned one class of colors, and positive numbers will be assigned another.
col_scale	One of c("green", "purple", "orange", "blue", "brown", "gray") to indicate the color scale to be used. Defaults to gray.
light_dark	One of "l", "d", or "f" indicating whether the colors used should be light ("l"), dark ("d"), or from across the full spectrum ("f").
grad_dir	A string specifying how the color gradient should be applied. If "high" higher values are given darker colors. If "low", lower values are given darker colors. If "middle" values in the middle of the spectrum are given darker colors, and if "end" values at the ends of the spectrum are given darker colors.
color_fun	Either "linear" or "exponential" indicating how the colors should transition from light to dark across values.
exp_steepness	If color_fun is "exponential," exp_steepness indicates how quickly the colors should transition from light to dark.
global_color_scale	Whether to impose a global minimum and maximum to the colors, or to use the values themselves to determine the top and bottom of the color scale.
global_min	If global_color_scale is TRUE, the minimum value that should be assigned a color.
global_max	If global_color_scale is TRUE, the maximum value that should be assigned a color.
use_pheatmap_colors	If TRUE, all other color parameters are ignored, and colors like those used in the R package pheatmap are used instead.
na_col	The color to use for missing values.

Value

A vector of colors assigned to the number is vals is returned.

References

Raivo Kolde (2019). pheatmap: Pretty Heatmaps. R package version 1.0.12. https://CRAN.R-project.org/package=pheatmap

TheJacksonLaboratory/cape documentation built on Feb. 12, 2024, 4:34 p.m.