[R-sig-phylo] Cannot read nexus tree from iTOL in R with read.nexus or read.tree

Dear All, I am trying to read a nexus tree created via iTOL into R. However, this is not to working. I am using the following tree:

Re: [R-sig-phylo] Cannot read nexus tree from iTOL in R with read.nexus or read.tree

Oops. I forgot one step - collapsing singleton nodes using collapse.singles in ape: library(phytools) ## text is your tree string tree-read.newick(text=text) tree-collapse.singles(tree) write.tree(phy=tree,file=Gudrun.tre) write.nexus(tree,file=Gudrun.nex) All the best, Liam Liam J. Revell,

[R-sig-phylo] Help with plot.phylo, how to extract the tips points coordinates and how to controle de plot area.

Hello. I'm trying to combine 2 plots, a phylogeny and a network. but i'm having a little problems. i have two question about the phylogeny plot and one about igraph, but about igraph i'll look for help on the package forum too, so no worries, but in case someone know igraph, the question is here

Re: [R-sig-phylo] Help with plot.phylo, how to extract the tips points coordinates and how to controle de plot area.

Thanks a lot guys, for all the answers. On the plot method of igraph, if i use rescale=F and i got the desired effect. Below are my code with the desired effect. I read the manual, but i think i did not notice the point, i think i got used to xlim argument and this mislead me to the confusion,