Re: [R-sig-phylo] Plotting character data next to tree in R

2017-01-13 Thread Liam J. Revell 

Hi Katharine.

You can try to search my blog for examples of the function 
add.simmap.legend. That might do what you want.


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 1/13/2017 10:57 AM, Katharine Walter wrote:

Hi,

I am trying to visualize a few different character traits on a tree using
phytools. My tiplabels are colored by sampling location and I'd like to add
alongside the tree a color bar that represents values of a discrete
character trait (bacterial serotypes) for each tip sample. There is a nice
explanation for how to do this for a continuous trait (
http://blog.phytools.org/2014/03/putting-barplot-next-to-plotted-tree.html)
and I'm wondering a way to visualize a discrete trait instead.

Thank you for your help!

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Re: [R-sig-phylo] multi2di fails on multiPhylo objects

2017-01-13 Thread Yan Wong 
On 13 Jan 2017, at 20:37, Klaus Schliep  wrote:

> Hi Yan,
> 
> it seems we introduced a small bug with making these functions generic. 
> Replace in the function .multi2di_ape the line   
> phy <- reorder(phy) 
> with 
> phy <- .reorder_ape(phy, "cladewise", FALSE, n, 1L)
> and it should work. You have to recompile ape afterwards. 

By the way, is this likely to make it into a new release soon, or is there a 
dev version I can access somehow? I need to roll this out across a number of 
different computers, some of which I don’t have admin access to.

Yan
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Re: [R-sig-phylo] multi2di fails on multiPhylo objects

2017-01-13 Thread Yan Wong 

On 13 Jan 2017, at 20:37, Klaus Schliep  wrote:

> Hi Yan,
> 
> it seems we introduced a small bug with making these functions generic. 
> Replace in the function .multi2di_ape the line   
> phy <- reorder(phy) 
> with 
> phy <- .reorder_ape(phy, "cladewise", FALSE, n, 1L)
> and it should work. You have to recompile ape afterwards. 

That’s great, thanks.

Yan
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Re: [R-sig-phylo] multi2di fails on multiPhylo objects

2017-01-13 Thread Klaus Schliep 
Hi Yan,

it seems we introduced a small bug with making these functions generic.
Replace in the function .multi2di_ape the line
phy <- reorder(phy)
with
phy <- .reorder_ape(phy, "cladewise", FALSE, n, 1L)
and it should work. You have to recompile ape afterwards.

Cheers,
Klaus





On Fri, Jan 13, 2017 at 1:24 PM, Yan Wong  wrote:

> Thanks. I think that’s because read_nexus_phylo() doesn’t do
> .compressTipLabel automatically
>
> n <- read_nexus_phylo("tmp.nex")
> n2 <- .compressTipLabel(n)
> multi2di(n2) #this causes an error.
>
> Unfortunately I need the .compressTipLabel functionality really.
>
> Yan
>
>
> On 13 Jan 2017, at 17:06, François Michonneau <
> francois.michonn...@gmail.com> wrote:
>
> > Hi Yan,
> >
> >  I'm not sure about what's going on here, but it works with the rncl
> > package (http://cran.r-project.org/web/packages/rncl/index.html)
> >
> >  install.packages("rncl")
> >  library(rncl)
> >  n <- read_nexus_phylo("tmp.nex")
>
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> sig-ph...@r-project.org/
>



-- 
Klaus Schliep
Postdoctoral Fellow
Revell Lab, University of Massachusetts Boston
http://www.phangorn.org/

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Re: [R-sig-phylo] multi2di fails on multiPhylo objects

2017-01-13 Thread Yan Wong 
Thanks. I think that’s because read_nexus_phylo() doesn’t do .compressTipLabel 
automatically

n <- read_nexus_phylo("tmp.nex")
n2 <- .compressTipLabel(n)
multi2di(n2) #this causes an error.

Unfortunately I need the .compressTipLabel functionality really.

Yan


On 13 Jan 2017, at 17:06, François Michonneau  
wrote:

> Hi Yan,
> 
>  I'm not sure about what's going on here, but it works with the rncl
> package (http://cran.r-project.org/web/packages/rncl/index.html)
> 
>  install.packages("rncl")
>  library(rncl)
>  n <- read_nexus_phylo("tmp.nex")

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Re: [R-sig-phylo] Amniote Phylogenetic Tree

2017-01-13 Thread François Michonneau 
Hi Sergio,

  You might find what you want within the Open Tree of Life
(http://tree.opentreeoflife.org/) whose content can be accessed from R
with the rotl package
(https://cran.r-project.org/web/packages/rotl/index.html)

  Cheers,
  -- François

On Fri, Jan 13, 2017 at 7:04 AM, Sergio Ferreira Cardoso
 wrote:
> Hello all,
>
> Do you know of any database where one can obtain a good phylogeny of the
> Amniota (in NEXUS or NEWICK file)?
> Thank you.
>
> Best regards,
> Sérgio.
>
> --
> Com os melhores cumprimentos,
> Sérgio Ferreira Cardoso.
>
> 
>
> Best regards,
> Sérgio Ferreira Cardoso
>
>
>
>
> MSc. Paleontology
> Museu da Lourinhã, GEAL.
> LATR/IST/CTN - Campus Tecnológico e Nuclear.
>
> Lisboa, Portugal
>
> [[alternative HTML version deleted]]
>
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[R-sig-phylo] Amniote Phylogenetic Tree

2017-01-13 Thread Sergio Ferreira Cardoso 
Hello all,

Do you know of any database where one can obtain a good phylogeny of the
Amniota (in NEXUS or NEWICK file)?
Thank you.

Best regards,
Sérgio.

-- 
Com os melhores cumprimentos,
Sérgio Ferreira Cardoso.



Best regards,
Sérgio Ferreira Cardoso




MSc. Paleontology
Museu da Lourinhã, GEAL.
LATR/IST/CTN - Campus Tecnológico e Nuclear.

Lisboa, Portugal

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[R-sig-phylo] Plotting character data next to tree in R

2017-01-13 Thread Katharine Walter 
Hi,

I am trying to visualize a few different character traits on a tree using
phytools. My tiplabels are colored by sampling location and I'd like to add
alongside the tree a color bar that represents values of a discrete
character trait (bacterial serotypes) for each tip sample. There is a nice
explanation for how to do this for a continuous trait (
http://blog.phytools.org/2014/03/putting-barplot-next-to-plotted-tree.html)
and I'm wondering a way to visualize a discrete trait instead.

Thank you for your help!

[[alternative HTML version deleted]]

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[R-sig-phylo] Introduction to R and statistics for biologists - CHINA - April2017

2017-01-13 Thread Oliver Hooker 

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[R-sig-phylo] multi2di fails on multiPhylo objects

2017-01-13 Thread Yan Wong 
If I have a nexus file with multiple trees, and the same tips in each tree, but 
some trees with polytomies, like this

#NEXUS
BEGIN TREES;
TRANSLATE
1 1,
2 2,
3 3,
4 4;
TREE A = (((1,2)5,3)6,4);
TREE B = ((1,2,3)6,4);
END;

Then when I try to resolve both trees using multi2di, I get

> n <- read.nexus("tmp.nex")
> multi2di(n)
Error in .reorder_ape(x, order, index.only, length(x$tip.label), io) : 
  tree apparently badly conformed

What am I doing wrong?
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