Hi Dave.

Yes. It is not perfect, but I have shown how to do this here: http://blog.phytools.org/2017/02/more-on-adding-error-bars-to-contmap.html.


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 2/27/2017 2:45 PM, David Bapst wrote:
That's really cool, Liam. Would it also be possible for one to do
multiple such error bars per node, for plotting ASRs for multiple
traits?
-Dave

On Mon, Feb 27, 2017 at 12:13 PM, Liam J. Revell <liam.rev...@umb.edu> wrote:
Hi Kevin.

This is not automatic - but it is indeed fairly easy to do using phytools.
To be honest, I thought this would look terrible - but it actually looks
much better than I expected, at least for a relatively small tree. I have
posted a demo to my blog here:
http://blog.phytools.org/2017/02/adding-colorful-error-bars-to-internal.html.

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 2/27/2017 11:16 AM, Arbuckle, Kevin wrote:

Hi all,

I was wondering about plotting the output of an ancestral state
'reconstruction' of a continuous trait while incorporating at least some of
the uncertainty around the estimates.

One approach I thought of was to map the ASR onto a tree in a standard
way, then at each node have essentially a mini-legend that is of a length
reflecting the width of the confidence interval of the estimate at that
node, and is coloured on the same colour-scale as the overall tree legend.
For instance, if the colour scheme for the tree goes from blue through
yellow to red as the value increases, then a node with a relatively precise
and high estimate will have a short bar only ranging through different
shades of red, whereas a highly uncertain low estimate will have a wider bar
coloured from (say) dark blue to orange/light red. I hope that description
makes sense.

I was wondering if anyone is aware of a function that already implements
such an approach, otherwise I'll try to put one together myself. I am aware
of phytool's fancyTree(type="phenogram95") as a way of incorporating
uncertainty into a plotted ASR for continuous traits. However, this often
results in difficulty in distinguishing different nodes where estimates are
similar and also does not lend itself easily to, for instance, plotting pie
charts representing discrete trait ASRs onto a tree mapped with a continuous
trait. Hence I can imagine a more general approach as above but don't want
to duplicate effort if a function already exists (and also if others feel
this is a useful idea it can be added to existing packages If I share it as
above).

Best wishes,
Kev
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