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Color Schemes

Source: vignettes/articles/color-schemes.Rmd
color-schemes.Rmd

Vizier makes use of the wonderful paletteer package which unifies the enormous number of palettes out there. To specify a color scheme, use the color_scheme parameter, passing one of:

  • A palette function that takes an integer n and returns a vector of colors, e.g. grDevices::rainbow.
  • A vector of colors making up a custom color scheme of your own devising, e.g. c('red', 'green', 'blue'). There must be at least two colors in the list.
  • The name of a color scheme provided by paletteer, in the form "package::palette". For a list of the many, many palettes supported, see paletteer’s github page. Some examples include "dutchmasters::milkmaid", "cartography::green.pal", "viridis::inferno", "RColorBrewer::Dark2". vizier makes no distinction between the continuous, fixed-width or dynamic palette classification used by paletteer.

For categories, a fully named color vector is a value-to-color mapping. This is useful when subsets or reordered factor levels should retain the same colors:

pca_iris <- stats::prcomp(iris[, -5], retx = TRUE, rank. = 2)
species_colors <- c(setosa = "#E69F00", versicolor = "#56B4E9", virginica = "#009E73")
embed_plot(pca_iris$x, iris$Species, color_scheme = species_colors)

Extra names are ignored, but every observed category must have a color. An unnamed vector remains a positional palette. The rev argument reverses a generated or named category palette before values are mapped; it does not reorder explicit per-observation colors supplied with colors.

Palette Interpolation

If the color scheme you select has a maximum number of colors, and vizier needs to use more than those that are available, then it will interpolate among the maximum number of colors to create the desired number. This may lead to results where different categories are hard to distinguish from each other. If you set verbose = TRUE, then if interpolation is required, a message will be logged to console to this effect. paletteer has information on the number of colors available in each palette.

Discrete Palettes with continuous Type

For discrete palettes, if you ask for fewer colors than the full range, you will only get the first few colors from the palette. For some palettes this works fine. For example, here is the Dark2 palette from RColorBrewer:

RColorBrewer Dark2 swatch
RColorBrewer Dark2 swatch

If you use this palette to color the iris PCA:

iris PCA with Dark2 color scheme
iris PCA with Dark2 color scheme

The three colors from the lefthand side of the swatch are used to color the species.

However, some discrete palettes have an ordering to them, e.g. they go from red to blue via yellow. Here’s rainbow from the jcolors package:

jcolors rainbow
jcolors rainbow

The PCA embedding now looks like:

iris PCA with rainbow color scheme
iris PCA with rainbow color scheme

If you would prefer to use a fuller extent of the palette, you can treat the palette as continuous, by appending ::c to the name of the color scheme, e.g. "jcolors::rainbow::c". Now the result is:

iris PCA with continuous rainbow color scheme
iris PCA with continuous rainbow color scheme

where the colors come from the left-most, right-most and center positions on the swatch.

The downside to treating these palettes as continuous is that there is no guarantee that the interpolation will result in colors that actually come from the palette. In fact, they probably won’t. We just got lucky in the above example, because interpolating between colors was not required. For colors which show a natural progression like jcolors::rainbow, results should still be ok. However, for palettes like RColorBrewer::Dark2, interpolation may not turn out so well. The iris PCA with the “continuous” version of Dark2, i.e. specifying RColorBrewer::Dark2::c results in:

iris PCA with continuous Dark2 color scheme
iris PCA with continuous Dark2 color scheme

The left cluster uses the green from the left-hand side of the Dark2 swatch, and the right cluster is colored in the gray color from the right-hand side. But the middle cluster isn’t any of the other colors and mixes rather murkily with the gray cluster. It doesn’t make sense to use interpolation in this case.

In summary, avoid interpolation of discrete color schemes if you can, and definitely do avoid for those like RColorBrewer::Dark2 which don’t work on a color scale.