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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