Hi Liam, That did solve that problem and now a tree is plotted. But it is just a plain tree without bars at the tips. Here's what I'm doing and the error I get:
> plotTree.wBars(tree=tr, x=dat, type='fan', scale=0.05, width=1, col='red') Error in if (min(x) < 0) h <- max(nodeHeights(tree)) : missing value where TRUE/FALSE needed I thought the problem might be that some of my trait values are negative. But apparently that's not it, because dat=dat-min(dat) doesn't solve the problem. Thanks, *--* *Rafael Sobral Marcondes* PhD Candidate (Systematics, Ecology and Evolution/Ornithology) Museum of Natural Science <http://sites01.lsu.edu/wp/mns/> Louisiana State University 119 Foster Hall Baton Rouge, LA 70803, USA Twitter: @rafmarcondes <https://twitter.com/rafmarcondes> On Fri, Nov 10, 2017 at 7:06 PM, Liam J. Revell <[email protected]> wrote: > Hi Rafael. > > It seems to just be that some of the values in your data vector are NAs. > > Try: > > dat<-dat[!is.na(dat)] > tr<-drop.tip(tr,setdiff(tr$tip.label,names(dat))) > plotTree.wBars(tr,dat,type="fan",scale=0.1) > > and you should obtain something that makes sense. > > All the best, Liam > > Liam J. Revell, Associate Professor of Biology > University of Massachusetts Boston > web: http://faculty.umb.edu/liam.revell/ > email: [email protected] > blog: http://blog.phytools.org > > On 11/10/2017 6:04 PM, Rafael S Marcondes wrote: > >> Hi Liam, >> >> Thanks for the quick reply. Playing with the scale argument didn't help. >> I have attached my script and environment. >> >> Thanks, >> >> *-- >> * >> *Rafael Sobral Marcondes* >> PhD Candidate (Systematics, Ecology and Evolution/Ornithology) >> >> Museum of Natural Science <http://sites01.lsu.edu/wp/mns/> >> Louisiana State University >> 119 Foster Hall >> Baton Rouge, LA 70803, USA >> >> Twitter: @rafmarcondes <https://twitter.com/rafmarcondes> >> >> >> On Fri, Nov 10, 2017 at 5:25 PM, Liam J. Revell <[email protected] >> <mailto:[email protected]>> wrote: >> >> Hello Rafael. >> >> Have you tried adjusting the argument 'scale' which sets the factor >> by which x will be rescaled so that the tree & data can be plotted >> in the same space? >> >> Also, if you are just plotting a right-facing phylogram I recommend >> plotTree.barplot (also within phytools) which is in some ways more >> flexible & robust. >> >> Failing any of these options you are welcome to send me your saved >> workspace so I can investigate (& if there is a bug in phytools - >> fix it). >> >> All the best, Liam >> >> Liam J. Revell, Associate Professor of Biology >> University of Massachusetts Boston >> web: http://faculty.umb.edu/liam.revell/ >> <http://faculty.umb.edu/liam.revell/> >> email: [email protected] <mailto:[email protected]> >> >> blog: http://blog.phytools.org >> >> On 11/10/2017 4:55 PM, Rafael S Marcondes wrote: >> >> Hi all, >> >> I'm encountering a little bump trying to use this really cool >> plot function >> in phytools and I can't figure out what's wrong: >> >> plotTree.wBars(tree=tr, x=dat) >> >> Error in plot.window(xlim = xlim, ylim = ylim, asp = asp) : >> need finite 'xlim' values >> >> Including an xlim argument doesn't work: >> >> plotTree.wBars(tree=tr, x=dat, xlim=c(0,100), ylim=c(0,100)) >> >> Error in plot.window(xlim = xlim, ylim = ylim, asp = asp) : >> need finite 'xlim' values >> >> Thanks for any help! >> >> >> *--* >> *Rafael Sobral Marcondes* >> PhD Candidate (Systematics, Ecology and Evolution/Ornithology) >> >> Museum of Natural Science <http://sites01.lsu.edu/wp/mns/ >> <http://sites01.lsu.edu/wp/mns/>> >> Louisiana State University >> 119 Foster Hall >> Baton Rouge, LA 70803, USA >> >> Twitter: @rafmarcondes <https://twitter.com/rafmarcondes >> <https://twitter.com/rafmarcondes>> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> R-sig-phylo mailing list - [email protected] >> <mailto:[email protected]> >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >> <https://stat.ethz.ch/mailman/listinfo/r-sig-phylo> >> Searchable archive at >> http://www.mail-archive.com/[email protected]/ >> <http://www.mail-archive.com/[email protected]/> >> >> >> [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/
