Description

Assigns Colours to Values.

Description

Maps one of the viridis colour palettes, or a user-specified palette to values. Viridis colour maps are created by Stéfan van der Walt and Nathaniel Smith, and were set as the default palette for the 'Python' 'Matplotlib' library <https://matplotlib.org/>. Other palettes available in this library have been derived from 'RColorBrewer' <https://CRAN.R-project.org/package=RColorBrewer> and 'colorspace' <https://CRAN.R-project.org/package=colorspace> packages.

README.md

cran.r-project.org

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colourvalues

What does it do?

It maps viridis colours (by default) to values, and quickly!

Note It does not perform a 1-to-1 mapping of a palette to values. It interpolates the colours from a given palette.

Why did you build it?

I’m aware there are other methods for mapping colours to values. And which do it quick too. But I can never remember them, and I find the interfaces a bit cumbersome. For example, scales::col_numeric(palette = viridisLite::viridis(5), domain = range(1:5))(1:5).

I wanted one function which will work on one argument.

colour_values(1:5)
# [1] "#440154FF" "#3B528BFF" "#21908CFF" "#5DC963FF" "#FDE725FF"
colour_values(letters[1:5])
# [1] "#440154FF" "#3B528BFF" "#21908CFF" "#5DC963FF" "#FDE725FF"

I also want it available at the src (C/C++) level for linking to other packages.

Why do you spell colour with a ‘u’?

Because it’s correct, and R tells us to

For consistency, aim to use British (rather than American) spelling

But don’t worry, color_values(1:5) works as well

How do I install it?

From CRAN

install.packages("colourvalues")

Or install the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("SymbolixAU/colourvalues")

How can I make use of it in my package?

Rcpp

All functions are written in Rcpp. I have exposed some of them in header files so you can “link to” them in your package.

For example, the LinkingTo section in DESCRIPTION will look something like

LinkingTo: 
    Rcpp,
    colourvalues

And in a c++ source file so you can #include the API header

#include "colourvalues/api.hpp"
// [[Rcpp::depends(colourvalues)]]

And call

// return hex colours
colourvalues::api::colour_values_hex()

// return RGP matrix
colourvalues::api::colour_values_rgb()

If you’re not using Rcpp, just Import this package like you would any other.

Do you have any examples?

Of course!

256 numbers mapped to a colour

bar_plot <- function(df) {
  barplot( height = df[["a"]], col = df[["col"]], border = NA, space = 0, yaxt = 'n')
}
df <- data.frame(a = 10, x = 1:256)
df$col <- colour_values(df$x, palette = "viridis")
bar_plot( df )

5000 numbers on a non-linear scale

df <- data.frame(a = 10, x = c((1:5000)**3))
df$col <- colour_values(df$x, palette = "viridis")
bar_plot( df )

1000 random numbers

df <- data.frame(a = 10, x = rnorm(n = 1000))
df$col <- colour_values(df$x, palette = "inferno")
bar_plot( df )

Eurgh!

df <- df[with(df, order(x)), ]
bar_plot( df )

That’s better!

Are there only viridis palettes?

No, you can chose one from

colour_palettes()
#  [1] "viridis"        "cividis"        "magma"          "inferno"       
#  [5] "plasma"         "ylorrd"         "ylorbr"         "ylgnbu"        
#  [9] "ylgn"           "reds"           "rdpu"           "purples"       
# [13] "purd"           "pubugn"         "pubu"           "orrd"          
# [17] "oranges"        "greys"          "greens"         "gnbu"          
# [21] "bupu"           "bugn"           "blues"          "spectral"      
# [25] "rdylgn"         "rdylbu"         "rdgy"           "rdbu"          
# [29] "puor"           "prgn"           "piyg"           "brbg"          
# [33] "terrain"        "topo"           "heat"           "cm"            
# [37] "rainbow"        "terrain_hcl"    "heat_hcl"       "sequential_hcl"
# [41] "rainbow_hcl"    "diverge_hcl"    "diverge_hsv"    "ygobb"         
# [45] "matlab_like2"   "matlab_like"    "magenta2green"  "cyan2yellow"   
# [49] "blue2yellow"    "green2red"      "blue2green"     "blue2red"

And you can use show_colours() to view them all. Here’s what some of them look like

show_colours( colours = colour_palettes(c("viridis", "colorspace")))

Do I have to use the in-built palettes?

No, you can use your own specified as a matrix of red, green and blue columns in the range [0,255]

n <- 100
m <- grDevices::colorRamp(c("red", "green"))( (1:n)/n )
df <- data.frame(a = 10, x = 1:n)
df$col <- colour_values(df$x, palette = m)
bar_plot( df )

Do you support ‘alpha’ values

Yep. Either supply a single alpha value for all the colours

## single alpha value for all colours
df <- data.frame(a = 10, x = 1:255)
df$col <- colour_values(df$x, alpha = 50)
bar_plot( df )

Or use a vector of values the same length as x

df <- data.frame(a = 10, x = 1:300, y = rep(c(1:50, 50:1), 3) )
df$col <- colour_values(df$x, alpha = df$y)
bar_plot( df )

Or include the alpha value as a 4th column in the palette matrix

n <- 100
m <- grDevices::colorRamp(c("red", "green"))( (1:n)/n )
## alpha values
m <- cbind(m, seq(0, 255, length.out = 100))
df <- data.frame(a = 10, x = 1:n)
df$col <- colour_values(df$x, palette = m)
bar_plot( df )

Some of my plotting functions don’t support alpha, can I exclude it?

Yep. Set include_alpha = FALSE

colour_values(1:5, include_alpha = F)
# [1] "#440154" "#3B528B" "#21908C" "#5DC963" "#FDE725"
colour_values_rgb(1:5, include_alpha = F)
#      [,1] [,2] [,3]
# [1,]   68    1   84
# [2,]   59   82  139
# [3,]   33  144  140
# [4,]   93  201   99
# [5,]  253  231   37

Can I get a summary of colours to use in a legend?

Yes, for numeric values use the n_summaries argument to specify the number of summary values you’d like

colour_values(1:10, n_summaries = 3)
# $colours
#  [1] "#440154FF" "#482878FF" "#3E4A89FF" "#31688EFF" "#26838EFF" "#1F9D89FF"
#  [7] "#35B779FF" "#6CCE59FF" "#B4DD2CFF" "#FDE725FF"
# 
# $summary_values
# [1] "1.00"  "5.50"  "10.00"
# 
# $summary_colours
# [1] "#440154FF" "#21908CFF" "#FDE725FF"

You can also specify the number of digits you’d like returned in the summary

colour_values(rnorm(n = 10), n_summaries = 3, digits = 2)
# $colours
#  [1] "#FDE725FF" "#440154FF" "#5CC863FF" "#3F4889FF" "#443A83FF" "#1E9D89FF"
#  [7] "#1E9C89FF" "#77D153FF" "#4EC36BFF" "#2D718EFF"
# 
# $summary_values
# [1] "-1.27" "0.36"  "1.99" 
# 
# $summary_colours
# [1] "#440154FF" "#21908CFF" "#FDE725FF"

You can also use format = FALSE if you don’t want the summary values formatted.

dte <- seq(as.Date("2018-01-01"), as.Date("2018-02-01"), by = 1)
colour_values(dte, n_summaries = 3)
# $colours
#  [1] "#440154FF" "#470D60FF" "#48196BFF" "#482474FF" "#472E7CFF" "#453882FF"
#  [7] "#414286FF" "#3E4B8AFF" "#3A548CFF" "#365D8DFF" "#32658EFF" "#2E6D8EFF"
# [13] "#2B758EFF" "#287D8EFF" "#25858EFF" "#228C8DFF" "#20948CFF" "#1E9C89FF"
# [19] "#20A386FF" "#25AB82FF" "#2DB27DFF" "#39BA76FF" "#48C16EFF" "#58C765FF"
# [25] "#6ACD5BFF" "#7ED34FFF" "#92D742FF" "#A8DB34FF" "#BEDF26FF" "#D4E21BFF"
# [31] "#E9E41AFF" "#FDE725FF"
# 
# $summary_values
# [1] "2018-01-01" "2018-01-16" "2018-02-01"
# 
# $summary_colours
# [1] "#440154FF" "#21908CFF" "#FDE725FF"

colour_values(dte, n_summaries = 3, format = F)
# $colours
#  [1] "#440154FF" "#470D60FF" "#48196BFF" "#482474FF" "#472E7CFF" "#453882FF"
#  [7] "#414286FF" "#3E4B8AFF" "#3A548CFF" "#365D8DFF" "#32658EFF" "#2E6D8EFF"
# [13] "#2B758EFF" "#287D8EFF" "#25858EFF" "#228C8DFF" "#20948CFF" "#1E9C89FF"
# [19] "#20A386FF" "#25AB82FF" "#2DB27DFF" "#39BA76FF" "#48C16EFF" "#58C765FF"
# [25] "#6ACD5BFF" "#7ED34FFF" "#92D742FF" "#A8DB34FF" "#BEDF26FF" "#D4E21BFF"
# [31] "#E9E41AFF" "#FDE725FF"
# 
# $summary_values
# [1] 17532.0 17547.5 17563.0
# 
# $summary_colours
# [1] "#440154FF" "#21908CFF" "#FDE725FF"

For categorical values use summary = TRUE to return a uniqe set of the values, and their associated colours

colour_values(sample(letters, size = 50, replace = T), summary = T)
# $colours
#  [1] "#277F8EFF" "#63CB5FFF" "#63CB5FFF" "#1FA187FF" "#3C4F8AFF" "#365C8DFF"
#  [7] "#FDE725FF" "#365C8DFF" "#1FA187FF" "#471365FF" "#365C8DFF" "#DFE318FF"
# [13] "#238A8DFF" "#3C4F8AFF" "#80D34DFF" "#46327FFF" "#35B779FF" "#471365FF"
# [19] "#440154FF" "#26AC81FF" "#1FA187FF" "#2C748EFF" "#63CB5FFF" "#FDE725FF"
# [25] "#80D34DFF" "#46327FFF" "#1F968BFF" "#BFDF25FF" "#3C4F8AFF" "#2C748EFF"
# [31] "#9FDA3AFF" "#31688EFF" "#4AC26DFF" "#4AC26DFF" "#3C4F8AFF" "#4AC26DFF"
# [37] "#35B779FF" "#9FDA3AFF" "#1FA187FF" "#26AC81FF" "#482374FF" "#1F968BFF"
# [43] "#26AC81FF" "#FDE725FF" "#4AC26DFF" "#3C4F8AFF" "#277F8EFF" "#35B779FF"
# [49] "#80D34DFF" "#424186FF"
# 
# $summary_values
#  [1] "b" "c" "d" "e" "f" "g" "h" "i" "j" "k" "m" "n" "o" "p" "q" "r" "s" "u" "v"
# [20] "w" "x" "y"
# 
# $summary_colours
#  [1] "#440154FF" "#471365FF" "#482374FF" "#46327FFF" "#424186FF" "#3C4F8AFF"
#  [7] "#365C8DFF" "#31688EFF" "#2C748EFF" "#277F8EFF" "#238A8DFF" "#1F968BFF"
# [13] "#1FA187FF" "#26AC81FF" "#35B779FF" "#4AC26DFF" "#63CB5FFF" "#80D34DFF"
# [19] "#9FDA3AFF" "#BFDF25FF" "#DFE318FF" "#FDE725FF"

I see you support lists, but how does it work?

Basically, it’s the same as un-listing the list to create a vector of all the values, then colouring them.

So if your list contains different types, it will coerce all values to the same type and colour them.

But it returns a list of the same structure.

For example,


l <- list( x = 1:5, y = list(z = letters[1:5] ) )
colour_values( l )
# [[1]]
# [1] "#440154FF" "#482878FF" "#3E4A89FF" "#31688EFF" "#26838EFF"
# 
# [[2]]
# [[2]][[1]]
# [1] "#1F9D89FF" "#35B779FF" "#6CCE59FF" "#B4DD2CFF" "#FDE725FF"

x <- c( 1:5, letters[1:5] )
colour_values( x )
#  [1] "#440154FF" "#482878FF" "#3E4A89FF" "#31688EFF" "#26838EFF" "#1F9D89FF"
#  [7] "#35B779FF" "#6CCE59FF" "#B4DD2CFF" "#FDE725FF"

What it doesn’t do is treat each list element independently. For this you would use

lapply( l, colour_values ) 
# $x
# [1] "#440154FF" "#3B528BFF" "#21908CFF" "#5DC963FF" "#FDE725FF"
# 
# $y
# $y[[1]]
# [1] "#440154FF" "#3B528BFF" "#21908CFF" "#5DC963FF" "#FDE725FF"

What’s the performance like?

10 million numeric values

library(microbenchmark)
library(scales)
library(viridisLite)

n <- 1e7
df <- data.frame(x = rnorm(n = n))

m <- microbenchmark(
  colourvalues = { colourvalues::colour_values(x = df$x) },
  scales = { col_numeric(palette = rgb(subset(viridis.map, opt=="D")[, 1:3]), domain = range(df$x))(df$x) },
  times = 25
)
# Warning in microbenchmark(colourvalues = {: less accurate nanosecond times to
# avoid potential integer overflows
m
# Unit: milliseconds
#          expr       min        lq      mean    median        uq       max neval
#  colourvalues  789.3592  797.2215  808.1314  805.4144  810.2691  866.7162    25
#        scales 1696.3621 1761.6745 1820.4097 1793.3245 1865.7442 2118.4543    25

1 million characters (26 unique values)

library(microbenchmark)
library(scales)
library(viridisLite)

n <- 1e6
x <- sample(x = letters, size = n, replace = TRUE)
df <- data.frame(x = x)

m <- microbenchmark(
  colourvalues = { x <- colourvalues::colour_values(x = df$x) },
  scales = { y <- col_factor(palette = rgb(subset(viridis.map, opt=="D")[, 1:3]), domain = unique(df$x))(df$x) },
  times = 25
)
m
# Unit: milliseconds
#          expr       min        lq      mean    median        uq      max neval
#  colourvalues  90.27962  90.81623  91.88558  90.93574  91.61257 104.2933    25
#        scales 195.65930 198.46062 203.90773 200.45052 204.15282 228.5454    25

r-colourvalues

colourvalues

What does it do?

Why did you build it?

Why do you spell colour with a ‘u’?

How do I install it?

How can I make use of it in my package?

Do you have any examples?

256 numbers mapped to a colour

5000 numbers on a non-linear scale

1000 random numbers

Are there only viridis palettes?

Do I have to use the in-built palettes?

Do you support ‘alpha’ values

Some of my plotting functions don’t support alpha, can I exclude it?

Can I get a summary of colours to use in a legend?

I see you support lists, but how does it work?

What’s the performance like?

Version

License

Status

Source

Homepage

Platforms (75)

colourvalues

What does it do?

Why did you build it?

Why do you spell colour with a ‘u’?

How do I install it?

How can I make use of it in my package?

Do you have any examples?

256 numbers mapped to a colour

5000 numbers on a non-linear scale

1000 random numbers

Are there only viridis palettes?

Do I have to use the in-built palettes?

Do you support ‘alpha’ values

Some of my plotting functions don’t support alpha, can I exclude it?

Can I get a summary of colours to use in a legend?

I see you support lists, but how does it work?

What’s the performance like?

Version

License

Status

Source

Homepage

Platforms75 (75)

Platforms (75)