Re: [R] getting 21 very different colours
Have a look at the Polychrome package by Kevin Coombes and Guy Brock: https://CRAN.R-project.org/package=Polychrome This employs the LUV space (with HCL = polar LUV) to get many distinct distinguishable colors. For a few first steps, see: https://CRAN.R-project.org/web/packages/Polychrome/vignettes/polychrome.html On Wed, 12 Sep 2018, Zach Simpson wrote: Hi Federico For a possible alternative, the scico package provides a nice collection of color palettes that are designed to be both color-blind friendly and differentiable: https://www.data-imaginist.com/2018/scico-and-the-colour-conundrum/ You could generate a vector of 21 colors (spaced as far apart as possible on the palette) to pass to your plot arguments with something like: library(scico) scico(21, palette = 'oleron') Not sure if this works for your case though. But maybe another feature (shape?) could help differentiate the 21 points. Hope this helps, Zach Simpson Message: 11 Date: Tue, 11 Sep 2018 07:34:51 + From: Federico Calboli To: "r-help@r-project.org" Subject: [R] getting 21 very different colours Message-ID: <08a6397b-4d67-4195-a53a-1fd394f72...@kuleuven.be> Content-Type: text/plain; charset="utf-8" Hi All, I am plotting a scatterplot of 21 populations, and I am using rainbow(21)[pops.col] to generate 21 colours for the plot (which works). Maybe it is because I can really process few colours at a time, but the differences between the colours are not as strong as I’d like. I can specify start and end for rainbow(), but if anything that looks worse if I do not just stick to 0 and 1. Is there a way of getting a set of 21 colours that maximises the differences between them? I could pick them by hand, but that is about 15 colours more than I know (I have a detailed colourchart, but the visual differences between ’skyblue’ and ’slategrey’ elude me when plotted as dots on a plot). Cheers F -- Federico Calboli LBEG - Laboratory of Biodiversity and Evolutionary Genomics Charles Deberiotstraat 32 box 2439 3000 Leuven +32 16 32 87 67 __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] getting 21 very different colours
Hi Federico For a possible alternative, the scico package provides a nice collection of color palettes that are designed to be both color-blind friendly and differentiable: https://www.data-imaginist.com/2018/scico-and-the-colour-conundrum/ You could generate a vector of 21 colors (spaced as far apart as possible on the palette) to pass to your plot arguments with something like: library(scico) scico(21, palette = 'oleron') Not sure if this works for your case though. But maybe another feature (shape?) could help differentiate the 21 points. Hope this helps, Zach Simpson > Message: 11 > Date: Tue, 11 Sep 2018 07:34:51 + > From: Federico Calboli > To: "r-help@r-project.org" > Subject: [R] getting 21 very different colours > Message-ID: <08a6397b-4d67-4195-a53a-1fd394f72...@kuleuven.be> > Content-Type: text/plain; charset="utf-8" > > Hi All, > > I am plotting a scatterplot of 21 populations, and I am using > rainbow(21)[pops.col] to generate 21 colours for the plot (which works). > Maybe it is because I can really process few colours at a time, but the > differences between the colours are not as strong as I’d like. I can specify > start and end for rainbow(), but if anything that looks worse if I do not > just stick to 0 and 1. > > Is there a way of getting a set of 21 colours that maximises the differences > between them? > > I could pick them by hand, but that is about 15 colours more than I know (I > have a detailed colourchart, but the visual differences between ’skyblue’ and > ’slategrey’ elude me when plotted as dots on a plot). > > Cheers > > F > -- > Federico Calboli > LBEG - Laboratory of Biodiversity and Evolutionary Genomics > Charles Deberiotstraat 32 box 2439 > 3000 Leuven > +32 16 32 87 67 __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] getting 21 very different colours
On Tue, Sep 11, 2018 at 11:43 AM, Duncan Murdoch wrote: > On 11/09/2018 3:34 AM, Federico Calboli wrote: > > Hi All, > > > > I am plotting a scatterplot of 21 populations, and I am using > rainbow(21)[pops.col] to generate 21 colours for the plot (which works). > Maybe it is because I can really process few colours at a time, but the > differences between the colours are not as strong as I’d like. I can > specify start and end for rainbow(), but if anything that looks worse if I > do not just stick to 0 and 1. > > > > Is there a way of getting a set of 21 colours that maximises the > differences between them? > > The LAB and LUV color spaces (in the colorspace package) attempt to map > perceptual differences to equal distances. You could try using a grid > of points in one of those spaces, but not all triples are valid. > > However, 21 colours is probably too many for your purpose. If you > really want to distinguish 21 groups, you're likely going to have to use > other characteristics as well, such as the symbol. You could plot 21 > different letters in 5 different colours and it might work, but it's not > going to be easy for viewers. > > The `alphabet` and `alphabet2` palettes from the `pals` package claim 26 "distinguishable" colours: Details: The ‘alphabet’ palette has 26 distinguishable colors that have logical names starting with the English alphabet letters A, B, ... Z. This palette is based on the work by Green-Armytage (2010), but uses the names 'orange' instead of 'orpiment', and 'magenta' instead of 'mallow'. There are some other palettes in that help page (?alphabet) that might also work. But 21 colours is pushing it. Barry > Duncan Murdoch > > > > > I could pick them by hand, but that is about 15 colours more than I know > (I have a detailed colourchart, but the visual differences between > ’skyblue’ and ’slategrey’ elude me when plotted as dots on a plot). > > > > Cheers > > > > F > > -- > > Federico Calboli > > LBEG - Laboratory of Biodiversity and Evolutionary Genomics > > Charles Deberiotstraat 32 box 2439 > > 3000 Leuven > > +32 16 32 87 67 > > > > > > > > > > > > __ > > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide http://www.R-project.org/ > posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. > > > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/ > posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] getting 21 very different colours
On 11/09/2018 3:34 AM, Federico Calboli wrote: Hi All, I am plotting a scatterplot of 21 populations, and I am using rainbow(21)[pops.col] to generate 21 colours for the plot (which works). Maybe it is because I can really process few colours at a time, but the differences between the colours are not as strong as I’d like. I can specify start and end for rainbow(), but if anything that looks worse if I do not just stick to 0 and 1. Is there a way of getting a set of 21 colours that maximises the differences between them? The LAB and LUV color spaces (in the colorspace package) attempt to map perceptual differences to equal distances. You could try using a grid of points in one of those spaces, but not all triples are valid. However, 21 colours is probably too many for your purpose. If you really want to distinguish 21 groups, you're likely going to have to use other characteristics as well, such as the symbol. You could plot 21 different letters in 5 different colours and it might work, but it's not going to be easy for viewers. Duncan Murdoch I could pick them by hand, but that is about 15 colours more than I know (I have a detailed colourchart, but the visual differences between ’skyblue’ and ’slategrey’ elude me when plotted as dots on a plot). Cheers F -- Federico Calboli LBEG - Laboratory of Biodiversity and Evolutionary Genomics Charles Deberiotstraat 32 box 2439 3000 Leuven +32 16 32 87 67 __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] getting 21 very different colours
On Tue, 11 Sep 2018 07:34:51 +
Federico Calboli wrote:
> Is there a way of getting a set of 21 colours that maximises the
> differences between them?
In my limited experience, getting even 10 colours to look different
enough is a serious undertaking. Take a look at RColorBrewer:
display.brewer.all(n, "qual") stops offering palettes for n>12.
When I needed a 10-colour categorical/qualitative palette, I opted for
brute force approach of maximising the minimal distance between points
in HCL colourspace, although later my colleague told me that I just
needed an existing algorithm to place the points uniformly. It has to
be HCL and not RGB because HCL signifies the way people perceive
different colours while RGB is only a good representation hardware-wise.
Here is my code; the usual disclaimers about stuff written between 1 and
3 AM apply:
# -8<---
require(nloptr)
h <- c(0,360)
c <- c(0,137) # see the warning about fixup in `?hcl`: not all HCL points are
representable in RGB
# NOTE: depending on your plot background, you may have to change at least
luminance range
l <- c(30,90)
npoints <- 24 # I had only 10 here
pts <- matrix(ncol=3, nrow=npoints, dimnames=list(NULL, c("h","c","l")))
pts[,"h"] <- runif(npoints, min=h[1], max=h[2])
pts[,"c"] <- runif(npoints, min=c[1], max=c[2])
pts[,"l"] <- runif(npoints, min=l[1], max=l[2])
lb <- cbind(h=rep(h[1],npoints), c=rep(c[1],npoints), l=rep(l[1],npoints))
ub <- cbind(h=rep(h[2],npoints), c=rep(c[2],npoints), l=rep(l[2],npoints))
obj <- function(x) {
pts[,c("h","c","l")] <- x
# somehow the best results were achieved by calculating Euclidean
distance from cylindrical coordinates
pts <- cbind(pts[,"c"]*sin(pts[,'h']/360*2*pi),
pts[,'c']*cos(pts[,'h']/360*2*pi), pts[,'l'])
d <- as.matrix(dist(pts))
diag(d) <- NA
# maximise minimal distance <=> minimize negative of minimal distance
-min(d, na.rm=T)
}
# the stopping criterion is a bit lame, but the objective function here is very
hard to minimize
# 1e6 iterations take a few minutes on a relatively modern desktop
sol <- nloptr(as.vector(pts), obj, lb=as.vector(lb), ub=as.vector(ub),
opts=list(algorithm="NLOPT_GN_CRS2_LM", maxeval=1e6))
pts[,c("h","c",'l')] <- sol$solution
plot(pts[,"c"] * sin(pts[,"h"]/360*2*pi), pts[,"c"] * cos(pts[,"h"]/360*2*pi),
col=hcl(pts[,"h"], pts[,"c"], l), pch=19, cex=2)
# -8<---
I couldn't get my code to produce 24 acceptably different colours, but
maybe you will succeed with a similar approach.
--
Best regards,
Ivan
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] getting 21 very different colours
You could look at combning a number of palettes from the RColorBrewer package to get the palette length you want. S Ellison > -Original Message- > From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Federico > Calboli > Sent: 11 September 2018 08:35 > To: r-help@r-project.org > Subject: [R] getting 21 very different colours > > Hi All, > > I am plotting a scatterplot of 21 populations, and I am using > rainbow(21)[pops.col] to generate 21 colours for the plot (which works). > Maybe it is because I can really process few colours at a time, but the > differences between the colours are not as strong as I’d like. I can specify > start and end for rainbow(), but if anything that looks worse if I do not just > stick to 0 and 1. > > Is there a way of getting a set of 21 colours that maximises the differences > between them? > > I could pick them by hand, but that is about 15 colours more than I know (I > have a detailed colourchart, but the visual differences between ’skyblue’ and > ’slategrey’ elude me when plotted as dots on a plot). > > Cheers > > F > -- > Federico Calboli > LBEG - Laboratory of Biodiversity and Evolutionary Genomics > Charles Deberiotstraat 32 box 2439 > 3000 Leuven > +32 16 32 87 67 > > > > > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting- > guide.html > and provide commented, minimal, self-contained, reproducible code. *** This email and any attachments are confidential. Any use, copying or disclosure other than by the intended recipient is unauthorised. If you have received this message in error, please notify the sender immediately via +44(0)20 8943 7000 or notify postmas...@lgcgroup.com and delete this message and any copies from your computer and network. LGC Limited. Registered in England 2991879. Registered office: Queens Road, Teddington, Middlesex, TW11 0LY, UK __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] getting 21 very different colours
Hi All, I am plotting a scatterplot of 21 populations, and I am using rainbow(21)[pops.col] to generate 21 colours for the plot (which works). Maybe it is because I can really process few colours at a time, but the differences between the colours are not as strong as I’d like. I can specify start and end for rainbow(), but if anything that looks worse if I do not just stick to 0 and 1. Is there a way of getting a set of 21 colours that maximises the differences between them? I could pick them by hand, but that is about 15 colours more than I know (I have a detailed colourchart, but the visual differences between ’skyblue’ and ’slategrey’ elude me when plotted as dots on a plot). Cheers F -- Federico Calboli LBEG - Laboratory of Biodiversity and Evolutionary Genomics Charles Deberiotstraat 32 box 2439 3000 Leuven +32 16 32 87 67 __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
