[adegenet-forum] Change Colors in Colorplot()

Jombart, Thibaut t.jombart at imperial.ac.uk
Mon Jan 27 13:32:20 CET 2014

Hi there, 

thanks for re-posting on the forum. 

The sign of scores being arbitrary, there's a bit of tweaking to be made here. For instance:
## using the example in the doc
xy <- expand.grid(1:10,1:10)
df <- data.frame(x=1:100, y=100:1, z=runif(100,0,100))
colorplot(xy,df,cex=10,main="colorplot: toy example") # default version

## tweaking colors by changing the signs
newdf <- df
newdf[,1] <- -newdf[,1]
colorplot(xy,newdf,cex=10,main="colorplot: toy example")

## another tweak
newdf[,2] <- -newdf[,2]
colorplot(xy,newdf,cex=10,main="colorplot: toy example")

## etc. 

There's 8 schemes in total for 3 variables. It may be useful to have a function allowing to select a particular scheme, but I've never coded it (simple, but I don't really have time to do this right away).


From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Romain Lehnebach Cirad [romain.lehnebach at cirad.fr]
Sent: 27 January 2014 12:18
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] Change Colors in Colorplot()

Hello everybody,

As a part of a study about dispersion and domestication of a cultivated
species, we used sPCA as complement of others analyses. More
specifically, we used colorplot() function based on the scores of the
third first global components.
In order to facilitate the reading of our future readers, we want to
keep the same colour scheme we used in other analyses. This colour
scheme depict geographical origins of our samples. Thus, we want to
produce a colorplot with colours according to other analyses.
I had a precise look on the construction of colorplot function, but I
can not find the way to modify the function in order to obtain the
expected colours ...
One way, I guess, is to modify the scores on each axis to obtain the
good RGB combination.
But, it seems, quite hard to find the good combination, since we used 3
axis ...

Any advices, ideas or suggestions are welcome.

Best regards.

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