Hi Jake, Liam and list,
I have used function ring() in APE (see help for ape::phydataplot) to do
this. It gives you full control over colours, transparency etc., but you'll
have to manually specify the inner and outer radii of each 'donut'.
>From my experience, block colours override the tree branches (the tree
disappears if time scale is plotted subsequently), while plotting the time
scale before plotting the tree makes it difficult to get the right
proportionality between the time scale and the branch lengths.
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