Hey all.
Been getting a little bit more familiar with R's ape package for phylogenetic analysis.
I am having a difficult time figuring out how to export the bootstrap node support with my tree. I am sure it's an easy answer, but Googling and the ape docos haven't been useful.
I'm currently just doing a NJ tree.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
# Predefine the tree building params
co1.out = 26
co1.nj.gen >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
Is there some way of associating the bootstraps (co1.nj.bs) with the phylo object (co1.nj.tr), such that when I export as a NEXUS file, and open in a program like FigTree, I can get my calculated node values?
Many thanks in advance!
~ Josh
OK! I finally figured it out.
These links were useful:
- https://ecomorph.wordpress.com/2014/10/09/phylogenetic-trees-in-r-4/
- http://stackoverflow.com/questions/22749634/how-to-append-bootstrapped-values-of-clusters-tree-nodes-in-newick-format-in
PHYLO objects in R have an "optional" slot for nodal labels (phylo$node.label). However, if you make your tree in R, by default this slot isn't there.
You can therefore append your bootstraps to your PHYLO object.
A red herring is, however, that for whatever reason the write.nexus function has issues exporting node labels using this approach. Instead, use write.tree.
So, after making your bootstraps, the code would look like this:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
# Add bootstraps to PHYLO object
co1.nj.tr$node.label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
When you open in FigTree, you will be asked what the node labels are -- tell it they are bootstraps!
OK! I finally figured it out.
These links were useful:
- https://ecomorph.wordpress.com/2014/10/09/phylogenetic-trees-in-r-4/
- http://stackoverflow.com/questions/22749634/how-to-append-bootstrapped-values-of-clusters-tree-nodes-in-newick-format-in
PHYLO objects in R have an "optional" slot for nodal labels (phylo$node.label). However, if you make your tree in R, by default this slot isn't there.
You can therefore append your bootstraps to your PHYLO object.
A red herring is, however, that for whatever reason the write.nexus function has issues exporting node labels using this approach. Instead, use write.tree.
So, after making your bootstraps, the code would look like this:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
# Add bootstraps to PHYLO object
co1.nj.tr$node.label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
When you open in FigTree, you will be asked what the node labels are -- tell it they are bootstraps!
@Shaun, there was a lot of frustrated R time to get to the conclusion.... :D
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