Question: Bootstrap values on the phylogenetic tree in Ape r package
1
gravatar for Denis
27 days ago by
Denis100
Denis100 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 • 116 views
ADD COMMENTlink modified 27 days ago • written 27 days ago by Denis100
1

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

ADD REPLYlink written 27 days ago by Jean-Karim Heriche20k

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 27 days ago • written 27 days ago by Denis100
2

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

ADD REPLYlink written 27 days ago by Benn7.1k
3
gravatar for Denis
27 days ago by
Denis100
Denis100 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 27 days ago • written 27 days ago by Denis100
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2123 users visited in the last hour