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

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