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 <liam.rev...@umb.edu>
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]]
>>
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>>
>>
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Attachment: SRLGlobal.pdf
Description: Adobe PDF document

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