In marcosci/cividis: Color Vision Deficiency Optimized Version Of Viridis

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cividis

Jamie R. Nuñez, Christopher R. Anderton, and Ryan S. Renslow recently introduced optimized color maps for the scientific community. This so-called "cividis" colormap is generated by optimizing the "viridis" colormap and is optimal for viewing by those with or without color vision deficiency (CVD), a different visual perception of colors that affects 8.5% of the human population. It is designed to be perfectly perceptually-uniform, both in regular form and also when converted to black-and-white, and can be perceived by readers with all forms of color blindness. The cividis colormap was developed as a Python module called "cmaputil".

Because of the high interest of the scientific community in R, we make this new colormap available as an R package!

This is how the colormap looks like in comparison to viridis colors and from the view of a blue-blind person:

n_col <- 128

img <- function(obj, nam) {
  image(1:length(obj), 1, as.matrix(1:length(obj)), col=obj, 
        main = nam, ylab = "", xaxt = "n", yaxt = "n",  bty = "n")
}

library(viridis)
library(scales)
library(colorspace)
library(dichromat)

par(mfrow=c(5, 1), mar=rep(1, 4))
img(rev(cividis(n_col)), "cividis")
img(rep("#FFFFFF", 128), nam = "")
img(rev(viridis(n_col)), "viridis")
img(rev(magma(n_col)), "magma")
img(dichromat(rev(cividis(n_col)), "tritan"), "cividis blue-blind (tritanopia)")

... and like this in action (coloring neutral landscape models from NLMR):

library(NLMR)
library(rasterVis)
library(ggplot2)
library(patchwork)
library(cividis)

# simulate NLM
x <- nlm_random(ncol = 100,
                nrow = 100)

x1 <- nlm_gaussianfield(ncol = 100,
                        nrow = 100,
                        autocorr_range = 30)

x2 <- nlm_mosaicfield(ncol = 100,
                      nrow = 100,
                      n = 30)

x3 <- nlm_curds(c(0.9, 0.6, 0.6), c(20, 10, 5))


gplot(x) +
 geom_tile(aes(fill = value)) +
 labs(x = "Easting",
      y = "Northing") +
 theme_nlm() +
 scale_fill_cividis(
    na.value = "transparent",
    name = "",
    guide = ggplot2::guide_colorbar(
      barheight = ggplot2::unit(40, units = "mm"),
      barwidth = ggplot2::unit(1, units = "mm"),
      draw.ulim = FALSE,
      title.hjust = 0.5,
      title.vjust = 1.5,
      label.hjust = 0.5
 )) -> p1


gplot(x1) +
 geom_tile(aes(fill = value)) +
 labs(x = "Easting",
      y = "Northing") +
 theme_nlm() +
 scale_fill_cividis(
    na.value = "transparent",
    name = "",
    guide = ggplot2::guide_colorbar(
      barheight = ggplot2::unit(40, units = "mm"),
      barwidth = ggplot2::unit(1, units = "mm"),
      draw.ulim = FALSE,
      title.hjust = 0.5,
      title.vjust = 1.5,
      label.hjust = 0.5
 )) -> p2


gplot(x2) +
 geom_tile(aes(fill = value)) +
 labs(x = "Easting",
      y = "Northing") +
 theme_nlm() +
 scale_fill_cividis(
    na.value = "transparent",
    name = "",
    guide = ggplot2::guide_colorbar(
      barheight = ggplot2::unit(40, units = "mm"),
      barwidth = ggplot2::unit(1, units = "mm"),
      draw.ulim = FALSE,
      title.hjust = 0.5,
      title.vjust = 1.5,
      label.hjust = 0.5
 )) -> p3


gplot(x3) +
 geom_tile(aes(fill = value)) +
 labs(x = "Easting",
      y = "Northing") +
 theme_nlm_discrete() +
 scale_fill_cividis(
    discrete = FALSE,
    na.value = "transparent",
    name = "",
    guide = ggplot2::guide_colorbar(
      barheight = ggplot2::unit(40, units = "mm"),
      barwidth = ggplot2::unit(1, units = "mm"),
      draw.ulim = FALSE,
      title.hjust = 0.5,
      title.vjust = 1.5,
      label.hjust = 0.5
 )) -> p4

p1 + p2 + p3 + p4 + plot_layout(ncol = 1)

Installation

To install the developmental version of cividis, use the following R code:

# install.packages("devtools")
devtools::install_github("marcosci/cividis")

Example

This is a basic example which shows you how to solve a common problem:

## basic example code

# load packages
library(NLMR)
library(rasterVis)
library(cividis)

# simulate NLM
x <- nlm_random(ncol = 100,
                nrow = 100)

# plot it
gplot(x) +
 geom_tile(aes(fill = value)) +
 labs(x = "Easting",
      y = "Northing") +
 theme_nlm() +
 scale_fill_cividis(
    na.value = "transparent",
    name = "",
    guide = ggplot2::guide_colorbar(
      barheight = ggplot2::unit(40, units = "mm"),
      barwidth = ggplot2::unit(1, units = "mm"),
      draw.ulim = FALSE,
      title.hjust = 0.5,
      title.vjust = 1.5,
      label.hjust = 0.5
 )) -> p1