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).
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