Hello, I plot two trees (they include branch lengths) like this: cophylo.full <- phytools::cophylo(tr1=full[[1]], tr2=full[[3]], assoc=(cbind(sort(full[[1]]$tip.label), sort(full[[3]]$tip.label))), rotate=TRUE) phytools::plot.cophylo(x=cophylo.full lwd=2, link.type="curved") This generally looks very nice, the only problem is that in both trees (they have over 100 tips) I have some branch lengths close to root, which are relatively long and some crown groups, where the branch lengths are very short and the figure is hard to read. As I do not need branch lengths for this display, I tried to remove branch lengths (full[[1]]$branch.length <- NULL), which helped, but still not perfect. To my surprise, in some clades, branch lengths were still relatively short and clustered. Then I tried several iterations of scaling the branch lengths with compute.brlen(), playing with the 'power' parameter. I was able to get good output, but I wonder if there is some possibility to do this automatically. Might be something like use.edge.length=FALSE in ape::cophyloplot (about phytools::cophylo I like the automatic rotation and curved connecting lines). Sincerely, V.
-- Vojtěch Zeisek https://trapa.cz/en/ Department of Botany, Faculty of Science Charles University, Prague, Czech Republic https://www.natur.cuni.cz/biology/botany/ Institute of Botany, Czech Academy of Sciences Průhonice, Czech Republic http://www.ibot.cas.cz/en/
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