Re: [R-sig-phylo] Error in plotTree.wBars() in phytools

2017-11-11 Thread Liam J. Revell 
Hi Rafael. When I load your workspace & run the following code I can 
produce the attached plot. Does this not work for you?


library(phytools)
dat<-dat[!is.na(dat)]
tips<-setdiff(tr$tip.label,names(dat))
tr<-drop.tip(tr,tips)
pdf(file="tree.pdf")
plotTree.wBars(tree=tr, x=dat, lwd=1, type='fan', scale=0.05,
width=0.35, col='red')
dev.off()

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 11/11/2017 10:49 AM, Rafael S Marcondes wrote:

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 
Louisiana State University
119 Foster Hall
Baton Rouge, LA 70803, USA

Twitter: @rafmarcondes 


On Fri, Nov 10, 2017 at 7:06 PM, Liam J. Revell > 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 >
Louisiana State University
119 Foster Hall
Baton Rouge, LA 70803, USA

Twitter: @rafmarcondes >


On Fri, Nov 10, 2017 at 5:25 PM, Liam J. Revell
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/

     >
     email: 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)

         Mu

Re: [R-sig-phylo] Error in plotTree.wBars() in phytools

2017-11-11 Thread Rafael S Marcondes 
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 
Louisiana State University
119 Foster Hall
Baton Rouge, LA 70803, USA

Twitter: @rafmarcondes 


On Fri, Nov 10, 2017 at 7:06 PM, Liam J. Revell  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 
>> Louisiana State University
>> 119 Foster Hall
>> Baton Rouge, LA 70803, USA
>>
>> Twitter: @rafmarcondes 
>>
>>
>> On Fri, Nov 10, 2017 at 5:25 PM, Liam J. Revell > > 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/
>> 
>> email: 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 > >
>> Louisiana State University
>> 119 Foster Hall
>> Baton Rouge, LA 70803, USA
>>
>> Twitter: @rafmarcondes > >
>>
>>  [[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/
>> 
>>
>>
>>

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Re: [R-sig-phylo] Error in plotTree.wBars() in phytools

2017-11-10 Thread Liam J. Revell 

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 
Louisiana State University
119 Foster Hall
Baton Rouge, LA 70803, USA

Twitter: @rafmarcondes 


On Fri, Nov 10, 2017 at 5:25 PM, Liam J. Revell > 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/

email: 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 >
Louisiana State University
119 Foster Hall
Baton Rouge, LA 70803, USA

Twitter: @rafmarcondes >

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Re: [R-sig-phylo] Error in plotTree.wBars() in phytools

2017-11-10 Thread Liam J. Revell 

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/
email: 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 
Louisiana State University
119 Foster Hall
Baton Rouge, LA 70803, USA

Twitter: @rafmarcondes 

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