Question: Plots two phylogenetic trees face to face
0
gravatar for luzglongoria
9 months ago by
luzglongoria20
luzglongoria20 wrote:

hi,

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)

Then,

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 • 339 views
ADD COMMENTlink written 9 months ago by luzglongoria20

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 9 months ago by jrj.healey13k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1734 users visited in the last hour