Question: Bootstrap values on the phylogenetic tree in Ape r package
1
gravatar for Denis
8 months ago by
Denis170
Denis170 wrote:

Hi there, I've constructed the tree with bootstrap supports in Ape package. But i'd prefer to get bootstrap values in percentage not in absolute number of replications. How can i do that in Ape?

phylogenetics R • 855 views
ADD COMMENTlink modified 8 months ago • written 8 months ago by Denis170
1

Access the values in the returned object and divide by the number of bootstrap samples.

ADD REPLYlink written 8 months ago by Jean-Karim Heriche21k

There is no slot named node.label in my object of class 'phylo' (i use ape 5.3). So i can not execute something like:

tree$node.label <- as.numeric(tree$node.label)/1000
ADD REPLYlink modified 8 months ago • written 8 months ago by Denis170
2

Maybe show then what you do have. Some code might also be useful.

ADD REPLYlink written 8 months ago by Benn7.9k
3
gravatar for Denis
8 months ago by
Denis170
Denis170 wrote:

I solved the issue by the R code:

plot(stree)
nodelabels(round(myBoots/1000*100),adj = 0.7)

where myBoots is numeric vector containing my bootstrap values

ADD COMMENTlink modified 8 months ago • written 8 months ago by Denis170
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