Re: [R-sig-phylo] Painting clades in a fan tree with bars

2017-02-05 Thread Liam J. Revell 

Hi Oscar.

You need to first use paintSubTree to 'paint' each of the clades you 
want to label with a different state.


e.g.:

tree<-paintSubTree(tree,node=104,state="Asterid_1")
tree<-paintSubTree(tree,node=191,state="Asterid_2")

and so on.

Then you should be able to use the method="plotSimmap" and colors 
arguments to color each subclade differently with plotTree.wBars.


If you need a function to find the common ancestor (parent node) of each 
subclade, you can use the function ape::getMRCA or phytools::findMRCA.


Let me know if you need more help. 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 2/5/2017 9:07 PM, Oscar Valverde wrote:

Hi everyone

I am trying to paint different clades in a tree with a set of values on
the tips. I used the function plotTree.wBars to plot and color the bars,
and used node labels to define important clades in my study. However,
for publication, the reviewers want me to remove the labels and use
colors instead to separate clades. However, I still could not figure out
how to do this from the plotTree.wBars function (tried the
method="plotSimmap", but I get an error

Error in plotSimmap(tree, type = "fan", ftype = if (tip.labels) "i" else
"off")

Attached an example of the tree I submitted so far. Any advice will be
greatly appreciated.


Oscar Valverde
Post Doctorate Associate
International Center on Tropical Botany
Florida International University

‘Anything else you’re interested in is not going to happen if you can’t
breathe the air and drink the water. Don’t sit this one out. Do
something. You are by accident of fate alive at an absolutely critical
moment in the history of our planet.’ ~Carl Sagan

On Fri, Jan 13, 2017 at 11:32 PM, Liam J. Revell > wrote:

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!

[[alternative HTML version deleted]]

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[R-sig-phylo] Painting clades in a fan tree with bars

2017-02-05 Thread Oscar Valverde 
Hi everyone

I am trying to paint different clades in a tree with a set of values on the
tips. I used the function plotTree.wBars to plot and color the bars, and
used node labels to define important clades in my study. However, for
publication, the reviewers want me to remove the labels and use colors
instead to separate clades. However, I still could not figure out how to do
this from the plotTree.wBars function (tried the method="plotSimmap", but I
get an error

Error in plotSimmap(tree, type = "fan", ftype = if (tip.labels) "i" else
"off")

Attached an example of the tree I submitted so far. Any advice will be
greatly appreciated.


Oscar Valverde
Post Doctorate Associate
International Center on Tropical Botany
Florida International University

‘Anything else you’re interested in is not going to happen if you can’t
breathe the air and drink the water. Don’t sit this one out. Do something.
You are by accident of fate alive at an absolutely critical moment in the
history of our planet.’ ~Carl Sagan

On Fri, Jan 13, 2017 at 11:32 PM, Liam J. Revell 
wrote:

> 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-plo
>> tted-tree.html)
>> and I'm wondering a way to visualize a discrete trait instead.
>>
>> Thank you for your help!
>>
>> [[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-ph...@r-project.org/
>>
>>
> ___
> R-sig-phylo mailing list - R-sig-phylo@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
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> sig-ph...@r-project.org/
>


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