Hi Liam, thanks for your message, Okay, I guess my objective is to order all of my nodes rather than edges either in ascending or descending order. It looks like ladderize will do this all at once rather than node by node with other commands. Thank you for pointing me towards that! In all of my googling since yesterday, ladderize never came across my radar.
Cheers, Zach On Thu, Aug 11, 2016 at 11:09 AM, Liam Revell <liam.rev...@umb.edu> wrote: > Hi Zach. > > > > What is your objective here? reorder.phylo reorders the edges in the > “phylo” object, but does not usually change the order in which the tips are > plotted. For that, you should look at ape::rotate or phytools::rotateNodes > (I believe), ape::ladderize, or the argument tips in phytools::plotTree. > > > > All the best, Liam > > > > -- > Liam J. Revell, Associate Professor of Biology > University of Massachussetts Boston > email: liam.rev...@umb.edu > web: http://faculty.umb.edu/liam.revell > > Sent from Outlook Mail for Windows 10 phone > > > > *From: *Zach Culumber <zculum...@gmail.com> > *Sent: *Thursday, August 11, 2016 10:48 AM > *To: *r-sig-phylo@r-project.org > *Subject: *[R-sig-phylo] Unable to reorder any phylo object with > reorder.phylo > > > Hi everyone, > > I seem to have an issue where I cannot get any trees (real data or > simulated trees) to reorder. I've tried a lot of different things > including updating packages, restarting R, using a different computer. My > real trees have 501 tips, but I'm having this issue even when I simulate > trees with just 25 or 50 tips. Currently using R 3.3.1 in Rstudio and APE > 3.5. I also came across the trick of using: > > phy <- read.tree(text=write.tree(phy)) > > but that didn't seem to work either. The structure of the my phylo > objects (my real trees and simulated trees) are fine when passed > through checkValidPhylo. Ultimately, if it were just one tree I > would do it in an outside program and just import the reordered tree, > but I'm wanting to apply a reordering function across a multiphylo > object. However, I can't seem to get a single tree > reordered! I'm pasting some code below which is pretty boiler plate > but *should* I believe work, but doesn't work for me. If anyone has > any thoughts or advice, I would appreciate it. > Thank you! > > #Simulate a single tree to test the reorder function > > tree1<-pbtree(n=500,scale=10,nsim=1) > > plot(tree1) > > #Reorder with pruningwise > > tree2<-reorder.phylo(tree1, "pruningwise") > > plot(tree2) > > > Zach > > -- > Zachary W. Culumber > Postdoctoral Research Associate > Kansas State University > Division of Biology > http://www.zwcresearch.com > > Coordinator > Centro de Investigaciones Científicas de las Huastecas Aguazarca > http://www.cichaz.org > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r- > sig-ph...@r-project.org/ > -- Zachary W. Culumber Postdoctoral Research Associate Kansas State University Division of Biology http://www.zwcresearch.com Coordinator Centro de Investigaciones Científicas de las Huastecas Aguazarca http://www.cichaz.org [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
