Question: Plots two phylogenetic trees face to face
gravatar for luzglongoria
2.0 years ago by
luzglongoria40 wrote:


I have two phylogenetic trees (extension .nex) and need to plot them face to face with links between them.

I have also done a .cvs file with the associations between these two trees.

However, when I try ro run the commands that I have found I got some error message:

two trees

tree.nex <- rtree(40) parasitetree.nex <- rtree(20)

creation of the association matrix:

association <- read.csv("assoc.csv") cophyloplot(tree.nex, parasitetree.nex, assoc = association, length.line = 4, space = 28, gap = 3)

then I get this error:

Error: $ operator is invalid for atomic vectors

If I try with:

trees<-read.tree("Tree.nex") tree.nex<-trees[[1]] parasitetree.nex<-trees[[2]] assoc<-read.csv("assoc.csv") obj<-cophylo(tree.nex,parasitetree.nex,assoc=assoc, print=TRUE)


Error in cophylo(tree.nex, parasitetree.nex, assoc = assoc, print = TRUE) : tr1 & tr2 should be objects of class "phylo".

Any help is more than welcome :)

trees phytools ape • 823 views
ADD COMMENTlink written 2.0 years ago by luzglongoria40

Not sure about your code solution, but you can do this with Dendroscope. What you're looking for (I think) are tanglegrams.

ADD REPLYlink written 2.0 years ago by Joe18k
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