EVOLUTION-MANAGER

Edit File: intro-to-viridis.Rmd

---
title: "The viridis color palettes"
author:
  - "Bob Rudis, Noam Ross and Simon Garnier"
date: "`r Sys.Date()`"
output: 
  rmarkdown::html_vignette:
    toc: true
    toc_depth: 1
vignette: >
  %\VignetteIndexEntry{Intro to the viridis color palette}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

# tl;dr

Use the color scales in this package to make plots that are pretty,
better represent your data, easier to read by those with colorblindness, and
print well in grey scale.

Install **viridis** like any R package:

```
install.packages("viridis")
library(viridis)
```

For base plots, use the `viridis()` function to generate a palette:

```{r setup, include=FALSE}
library(viridis)
knitr::opts_chunk$set(echo = TRUE, fig.retina=2, fig.width=7, fig.height=5)
```

```{r tldr_base, message=FALSE}
x <- y <- seq(-8*pi, 8*pi, len = 40)
r <- sqrt(outer(x^2, y^2, "+"))
filled.contour(cos(r^2)*exp(-r/(2*pi)), 
               axes=FALSE,
               color.palette=viridis,
               asp=1)
```

For ggplot, use `scale_color_viridis()` and `scale_fill_viridis()`:

```{r, tldr_ggplot, message=FALSE}
library(ggplot2)
ggplot(data.frame(x = rnorm(10000), y = rnorm(10000)), aes(x = x, y = y)) +
  geom_hex() + coord_fixed() +
  scale_fill_viridis() + theme_bw()
```

# Introduction

The [**viridis**](https://cran.r-project.org/package=viridis) package
brings to R color scales created by [Stéfan van der Walt](https://github.com/stefanv) and [Nathaniel Smith](https://github.com/njsmith) for the Python **matplotlib** library.

These color scales are designed to be:

- **Colorful**, spanning as wide a palette as possible so as to make differences easy to see,
- **Perceptually uniform**, meaning that values close to each other have similar-appearing colors and values far away from each other have more different-appearing colors, consistently across the range of values,
- **Robust to colorblindness**, so that the above properties hold true for people with common forms of colorblindness, as well as in grey scale printing, and
- **Pretty**, oh so pretty

If you want to know more about the science behind creating these color scales, van
der Walt and Smith's [talk at SciPy 2015](https://www.youtube.com/watch?list=PLYx7XA2nY5Gcpabmu61kKcToLz0FapmHu&v=xAoljeRJ3lU) (YouTube) is quite interesting. On the project [website](http://bids.github.io/colormap/) you will find more details and a Python tool for creating other scales with similar properties.

# The Color Scales

The package contains four color scales: "Viridis", the primary choice, and three 
alternatives with similar properties, "magma", "plasma", and "inferno."

```{r for_repeat, include=FALSE}
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")
}
```

```{r begin, message=FALSE, include=FALSE}
library(viridis)
library(scales)
library(colorspace)
library(dichromat)
```

```{r show_scales, echo=FALSE,fig.height=3.575}
par(mfrow=c(5, 1), mar=rep(1, 4))
img(rev(viridis(n_col)), "viridis")
img(rev(magma(n_col)), "magma")
img(rev(plasma(n_col)), "plasma")
img(rev(inferno(n_col)), "inferno")
img(rev(cividis(n_col)), "cividis")
```

# Comparison

Let's compare the viridis and magma scales against these other commonly used sequential color
palettes in R:

- Base R palettes: `rainbow.colors`, `heat.colors`, `cm.colors`
- The default **ggplot2** palette
- Sequential [colorbrewer](http://colorbrewer2.org/) palettes, both default blues and
  the more viridis-like yellow-green-blue

```{r 01_normal, echo=FALSE}
par(mfrow=c(7, 1), mar=rep(1, 4))
img(rev(rainbow(n_col)), "rainbow")
img(rev(heat.colors(n_col)), "heat")
img(rev(seq_gradient_pal(low = "#132B43", high = "#56B1F7", space = "Lab")(seq(0, 1, length=n_col))), "ggplot default")
img(gradient_n_pal(brewer_pal(type="seq")(9))(seq(0, 1, length=n_col)), "brewer blues")
img(gradient_n_pal(brewer_pal(type="seq", palette = "YlGnBu")(9))(seq(0, 1, length=n_col)), "brewer yellow-green-blue")
img(rev(viridis(n_col)), "viridis")
img(rev(magma(n_col)), "magma")
```

It is immediately clear that the "rainbow" palette is not perceptually uniform;
there are several "kinks" where the apparent color changes quickly over a short
range of values.  This is also true, though less so, for the "heat" colors.
The other scales are more perceptually uniform, but "viridis" stands out for its
large *perceptual range*. It makes as much use of the available color space as
possible while maintaining uniformity.

Now, let's compare these as they might appear under various forms of colorblindness,
which can be simulated using the **[dichromat](https://cran.r-project.org/package=dichromat)** package:

### Green-Blind (Deuteranopia)

```{r 02_deutan, echo=FALSE}
par(mfrow=c(7, 1), mar=rep(1, 4))
img(dichromat(rev(rainbow(n_col)), "deutan"), "rainbow")
img(dichromat(rev(heat.colors(n_col)), "deutan"), "heat")
img(dichromat(rev(seq_gradient_pal(low = "#132B43", high = "#56B1F7", space = "Lab")(seq(0, 1, length=n_col))), "deutan"), "ggplot default")
img(dichromat(gradient_n_pal(brewer_pal(type="seq")(9))(seq(0, 1, length=n_col)), "deutan"), "brewer blues")
img(dichromat(gradient_n_pal(brewer_pal(type="seq", palette = "YlGnBu")(9))(seq(0, 1, length=n_col)), "deutan"), "brewer yellow-green-blue")
img(dichromat(rev(viridis(n_col)), "deutan"), "viridis")
img(dichromat(rev(magma(n_col)), "deutan"), "magma")
```

### Red-Blind (Protanopia)

```{r 03_protan, echo=FALSE}
par(mfrow=c(7, 1), mar=rep(1, 4))
img(dichromat(rev(rainbow(n_col)), "protan"), "rainbow")
img(dichromat(rev(heat.colors(n_col)), "protan"), "heat")
img(dichromat(rev(seq_gradient_pal(low = "#132B43", high = "#56B1F7", space = "Lab")(seq(0, 1, length=n_col))), "protan"), "ggplot default")
img(dichromat(gradient_n_pal(brewer_pal(type="seq")(9))(seq(0, 1, length=n_col)), "protan"), "brewer blues")
img(dichromat(gradient_n_pal(brewer_pal(type="seq", palette = "YlGnBu")(9))(seq(0, 1, length=n_col)), "protan"), "brewer yellow-green-blue")
img(dichromat(rev(viridis(n_col)), "protan"), "viridis")
img(dichromat(rev(magma(n_col)), "protan"), "magma")
```

### Blue-Blind (Tritanopia)

```{r 04_tritan, echo=FALSE}
par(mfrow=c(7, 1), mar=rep(1, 4))
img(dichromat(rev(rainbow(n_col)), "tritan"), "rainbow")
img(dichromat(rev(heat.colors(n_col)), "tritan"), "heat")
img(dichromat(rev(seq_gradient_pal(low = "#132B43", high = "#56B1F7", space = "Lab")(seq(0, 1, length=n_col))), "tritan"), "ggplot default")
img(dichromat(gradient_n_pal(brewer_pal(type="seq")(9))(seq(0, 1, length=n_col)), "tritan"), "brewer blues")
img(dichromat(gradient_n_pal(brewer_pal(type="seq", palette = "YlGnBu")(9))(seq(0, 1, length=n_col)), "tritan"), "brewer yellow-green-blue")
img(dichromat(rev(viridis(n_col)), "tritan"), "viridis")
img(dichromat(rev(magma(n_col)), "tritan"), "magma")
```

### Desaturated

```{r 05_desatureated, echo=FALSE}
par(mfrow=c(7, 1), mar=rep(1, 4))
img(desaturate(rev(rainbow(n_col))), "rainbow")
img(desaturate(rev(heat.colors(n_col))), "heat")
img(desaturate(rev(seq_gradient_pal(low = "#132B43", high = "#56B1F7", space = "Lab")(seq(0, 1, length=n_col)))), "ggplot default")
img(desaturate(gradient_n_pal(brewer_pal(type="seq")(9))(seq(0, 1, length=n_col))), "brewer blues")
img(desaturate(gradient_n_pal(brewer_pal(type="seq", palette = "YlGnBu")(9))(seq(0, 1, length=n_col))), "brewer yellow-green-blue")
img(desaturate(rev(viridis(n_col))), "viridis")
img(desaturate(rev(magma(n_col))), "magma")
```

We can see that in these cases, "rainbow" is quite problematic - it is not
perceptually consistent across its range.  "Heat" washes
out at bright colors, as do the brewer scales to a lesser extent. The ggplot scale
does not wash out, but it has a low perceptual range - there's not much contrast
between low and high values.  The "viridis" and "magma" scales do better - they cover a wide perceptual range in brightness in brightness and blue-yellow, and do not rely as much on red-green contrast. They do less well
under tritanopia (blue-blindness), but this is an extrememly rare form of colorblindness.

# Usage

The `viridis()` function produces the viridis color scale.  You can choose
the other color scale options using the `option` parameter or the convenience
functions `magma()`, `plasma()`, and `inferno()`.

Here the `inferno()` scale is used for a raster of U.S. max temperature:

```{r tempmap, message=FALSE}
library(rasterVis)
library(httr)
par(mfrow=c(1,1), mar=rep(0.5, 4))
temp_raster <- "http://ftp.cpc.ncep.noaa.gov/GIS/GRADS_GIS/GeoTIFF/TEMP/us_tmax/us.tmax_nohads_ll_20150219_float.tif"
try(GET(temp_raster,
        write_disk("us.tmax_nohads_ll_20150219_float.tif")), silent=TRUE)
us <- raster("us.tmax_nohads_ll_20150219_float.tif")
us <- projectRaster(us, crs="+proj=aea +lat_1=29.5 +lat_2=45.5 +lat_0=37.5 +lon_0=-96 +x_0=0 +y_0=0 +ellps=GRS80 +datum=NAD83 +units=m +no_defs")
image(us, col=inferno(256), asp=1, axes=FALSE, xaxs="i", xaxt='n', yaxt='n', ann=FALSE)
```

The package also contains color scale functions for **ggplot**
plots: `scale_color_viridis()` and `scale_fill_viridis()`.  As with `viridis()`, you can use the other scales with the `option` argument
in the `ggplot` scales.  Here the "magma" scale is used for a cloropleth
map of U.S. unemployment:

```{r, ggplot2}
unemp <- read.csv("http://datasets.flowingdata.com/unemployment09.csv",
                  header = FALSE, stringsAsFactors = FALSE)
names(unemp) <- c("id", "state_fips", "county_fips", "name", "year",
                  "?", "?", "?", "rate")
unemp$county <- tolower(gsub(" County, [A-Z]{2}", "", unemp$name))
unemp$county <- gsub("^(.*) parish, ..$","\\1", unemp$county)
unemp$state <- gsub("^.*([A-Z]{2}).*$", "\\1", unemp$name)

county_df <- map_data("county", projection = "albers", parameters = c(39, 45))
names(county_df) <- c("long", "lat", "group", "order", "state_name", "county")
county_df$state <- state.abb[match(county_df$state_name, tolower(state.name))]
county_df$state_name <- NULL

state_df <- map_data("state", projection = "albers", parameters = c(39, 45))

choropleth <- merge(county_df, unemp, by = c("state", "county"))
choropleth <- choropleth[order(choropleth$order), ]

ggplot(choropleth, aes(long, lat, group = group)) +
  geom_polygon(aes(fill = rate), colour = alpha("white", 1 / 2), size = 0.2) +
  geom_polygon(data = state_df, colour = "white", fill = NA) +
  coord_fixed() +
  theme_minimal() +
  ggtitle("US unemployment rate by county") +
  theme(axis.line = element_blank(), axis.text = element_blank(),
        axis.ticks = element_blank(), axis.title = element_blank()) +
  scale_fill_viridis(option="magma")
```

The ggplot functions also can be used for discrete scales with the argument
`discrete=TRUE`.

```{r discrete}
p <- ggplot(mtcars, aes(wt, mpg))
p + geom_point(size=4, aes(colour = factor(cyl))) +
    scale_color_viridis(discrete=TRUE) +
    theme_bw()
```

# Gallery

Here are some examples of viridis being used in the wild:

[James Curley](https://twitter.com/jalapic) uses **viridis** for matrix plots ([Code](https://gist.github.com/jalapic/9a1c069aa8cee4089c1e)):

[![](http://pbs.twimg.com/media/CQWw9EgWsAAoUi0.png)](https://twitter.com/jalapic/status/650120284901634048/photo/1)

[Jeff Hollister](https://twitter.com/jhollist) uses the viridis as a discrete categorical scale ([Code](http://github.com/USEPA/LakeTrophicModelling/blob/master/vignettes/manuscript.Rmd#cbpalette---c0072b2999999f0e442d55e00)):

[![](http://github.com/USEPA/LakeTrophicModelling/blob/master/vignettes/manuscript_files/figure-latex/gis_probability_map-1.jpeg?raw=TRUE)](http://github.com/USEPA/LakeTrophicModelling/blob/master/vignettes/manuscript_files/figure-latex/gis_probability_map-1.jpeg)

[Christopher Moore](https://twitter.com/lifedispersing) created these contour 
plots of potential in a dynamic plankton-consumer model:

[![](http://pbs.twimg.com/media/CQWTy7wWcAAa-gu.jpg)](https://twitter.com/lifedispersing/status/650088228016508928/photo/1)