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tree$edge does not reconcile with phylotree() data.frame #1
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Dear Mark Thanks for your comment. Hmm, that seems to go terribly wrong indeed. Cheers Mark Schultz schreef op 2016-08-30 06:32:
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Hi Mark
The issue is solved. It turns out that the phylo-class tree was the
wrong tree.
Cheers
Don
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Fixed! Thanks Don. |
Merge fix for sequence likelihood calculation at root coalescent node
Hi,
Thanks for the software. It looks like it will be very useful for us.
I'm trying to use it to plot an MCC tree with posterior support values overlaid. In the example below, I create the phybreak object using
phybreak(data, times)
. I burnin with 1000 cycles and sample for 10000 cycles.Then, I get the the phylotree() data.frame and tree:
My aim is to overlay the posterior supports from the phylo_tree_matrix on the phylo_tree, but the
phylo_tree$edge
matrix and thephylo_tree_matrix$parent
columns are irreconcilable, as can be found when comparing the plot of the tree (withtiplabels()
andnodelabels()
) with the following two tables:That is, the parent-child relationships between the following two tables do not align. Here is the edge table (the blue squares are column 1 and the yellow squares are column 2):
And here is the data.frame (rows 35, 36, 38, 39, 42, 43, 47 have bad parent-child relationships, where child is the row-name and parent is the corresponding cell value in column 1) :
I have seen in http://rpackages.ianhowson.com/cran/phybreak/man/phylotree.html that the phylotree data.frame should be: "A
data.frame
with per item (=node) its parent and support per clade, and optionally summary node times. The firstn
nodes are the samples, the lastn-1
nodes are the internal nodes." But, still, this does not seem to add up correctly.Is this an error or am I missing something? Could you please add a feature that adds these posterior support values to the tree (phylo) object
tree$node.label
so that I don't need to manually try to do this myself?Also, will be adding more to the documentation and providing tutorials? This would also be very helpful.
All the best,
Mark
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