Hi Martin. The solution of Gopal will work to change the color scheme of the 'densityMap' object, but this is also automated in the function setMap.
For example (in which trees is our 'multiSimmap' object):
obj<-densityMap(trees,res=200,plot=FALSE)
plot(obj) ## original color gradient
obj<-setMap(obj,invert=TRUE)
plot(obj) ## flipped color gradient
obj<-setMap(obj,c("blue","green","yellow"))
plot(obj,outline=TRUE,lwd=4) ## arbitrary gradient
However, you have probably noted that the function plots the posterior
probability of being in a given state, by default the alphanumerically
second of the two mapped states. This can also be changed as follows (in
which x is our trait vector):
ss<-sort(unique(x))[2:1] obj<-densityMap(trees,res=200,plot=FALSE,states=ss) plot(obj)In this case what should be plotted is the posterior probability of being in the alphanumerically first state, rather than the second.
All the best, Liam Liam J. Revell Associate Professor, University of Massachusetts Boston Profesor Asistente, Universidad Católica de la Ssma Concepción web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org On 9/26/2018 9:23 AM, Gopal Murali wrote:
Hi Martin, The below code might help you.require(phytools) tree<-pbtree(n=100) # simulate tree s<-sample(c(0,1),100,replace = T) # create character state names(s)<-tree$tip.label # assign tip labels to character state mtreel<-make.simmap(tree,s,nsim=10) XX <- densityMap(mtreel, lwd =2,ftype="off") s<-colorRampPalette(c("green","red")) # change the colors here XX$cols[]<-s(length(XX$cols)) plot(XX, lwd = 2,ftype="off",outline=FALSE) Regards, Gopal Murali --------------------------------------------------------------------- *“**How strange is the lot of us mortals! Each of us is here for a brief sojourn; for what purpose he knows not, though he sometimes thinks he senses it. But without deeper reflection one knows from daily life that one exists for other people…a hundred times every day I remind myself that my inner and outer life are based on the labors of other men, living and dead, and that I must exert myself in order to give in the same measure as I have received and am stillreceiving,”* ― Albert Einstein <http://www.goodreads.com/author/show/9810.Albert_Einstein> -------------------------------------------------------------------------------------On Wed, Sep 26, 2018 at 5:36 PM <rami...@macn.gov.ar> wrote:Hello, I want to change the colors of a Bayesian stochastic mapping, using make.simmap (e.g., switching blue and red). Is it possible? (I tried switching the order of the columns of the states -- no effect.) Thanks for any help! Martin Ramirez _______________________________________________ R-sig-phylo mailinglist - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchablearchive at http://www.mail-archive.com/r-sig-phylo@r-project.org/[[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailinglist - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archiveat http://www.mail-archive.com/r-sig-phylo@r-project.org/
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