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root function loses tip.label and node.label #120
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I also tried an older version treeio_1.20.2 (on a different computer) and this time, the tip.label and node.labels are retained. So something went wrong between versions 1.20.2 and version 1.26.0. |
I can reproduce the error on treeio 1.25.4 |
actually, not so sure that treeio_1.20.2 does work as I said on Friday. Now that I'm back on the first computer, and I've installed treeio_1.20.2 here, I still have a problem. Might be some interaction with one of the other packages I have installed - I'm a little unclear on what's going on under the hood, and which package(s) are most relevant. I guess my first question is - should I expect |
I figured out a workaround for this issue in my code: I go back to the tree as a plain phylo object, reroot that, and regenerate the treedata object by adding the metadata. Interestingly, when I plot the new rerooted trees (using Was there an error before in the 'root' method for treedata objects with node labels? Is that why node.labels are dropped now? I can't figure out how to make a reproducible example for the possibly wrongly placed node labels now that I've updated my R packages (because |
Hello, I can offer more detail, I tried to read the code of if checking the code of treeio:::build_new_tree:
I used same data as @jayoung , here is the content of
but after ran
I don't know whether this is correct class type for |
The same problem has occured in version 1.30.0 when using the root() to reroot the tree. As write in the ggtree book, (https://yulab-smu.top/treedata-book/chapter2.html?q=root#reroot-treeio)
The root() in treeio can't handdle the the treedata object. |
hi there,
I am trying to reroot a treedata object, and I find that the tip.label and node.labels are getting lost from the phylogeny (they're getting replaced with
c("1","2","3",etc)
The example code below should show you what I mean. I get the same problem if I use the trda treedata object defined in the treedata book
Am I doing something wrong, or is this a bug?
thanks very much!
Janet Young
Here's sessionInfo() output:
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