map_nodes_ott: Add Open Tree of Life Taxonomy to tree nodes.

In datelife: Scientific Data on Time of Lineage Divergence for Your Taxa

Add Open Tree of Life Taxonomy to tree nodes.

Description

Add Open Tree of Life Taxonomy to tree nodes.

Usage

map_nodes_ott(tree)

Arguments

tree	A tree either as a newick character string or as a phylo object.

Value

A phylo object with "nodelabels".

Examples

## Not run:  # This is a flag for package development. You are welcome to run the example.

# Load the Open Tree chronograms database cached in datelife:
utils::data(opentree_chronograms)

# Get the small chronograms (i.e., chronograms with less that ten tips) to generate a pretty plot:
small <- opentree_chronograms$trees[unlist(sapply(opentree_chronograms$trees, ape::Ntip)) < 10]

# Now, map the Open Tree taxonomy to the nodes of the first tree
phy <- map_nodes_ott(tree = small[[1]])
# and plot it:
# plot_phylo_all(phy)
library(ape)
plot(phy)
nodelabels(phy$node.label)


## End(Not run) #end dontrun

datelife documentation built on July 10, 2023, 2:02 a.m.