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: liam.rev...@umb.edu
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 <liam.rev...@umb.edu
<mailto:liam.rev...@umb.edu>> 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: liam.rev...@umb.edu <mailto:liam.rev...@umb.edu>
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>>
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