Coerce phylogenetic trees to phyloXML documents, objects of class xml_document
.
write_phyloxml(tree, ...) # S3 method for phylo write_phyloxml(tree, name = "A phylogenetic tree", description = "Some description", xmlns = "http://www.phyloxml.org", digits = 20, ...)
tree | A phylogenetic tree. |
---|---|
... | Further arguments to be passed to the method (see details). |
name | Character scalar. Name of the tree. |
description | Character scalar. Description of the tree. |
xmlns | Character scalar. Location of the default namespace (see the XML Namespaces section in w3schools). |
digits | Integer scalar. Precision to use when writing numbers. |
An XML document (see xml2::read_xml)
So far, this function has a method for phylo objects
from the ape
package. The following elements are supported:
Branch lengths as stored in edge.length
Labels, which are exported as name
, as stored in tip.label
and, if
available, Node.label
.
Tree topology as stored in edges
Han M.V. and Zmasek C.M. (2009) "phyloXML: XML for evolutionary biology and comparative genomics" BMC Bioinformatics, 10:356 doi:10.1186/1471-2105-10-356
# Random tree from the ape package ------------------------------------------ set.seed(1) x <- ape::rtree(5) x#> #> Phylogenetic tree with 5 tips and 4 internal nodes. #> #> Tip labels: #> [1] "t3" "t4" "t1" "t2" "t5" #> #> Rooted; includes branch lengths.write_phyloxml(x)#> {xml_document} #> <phyloxml schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://www.phyloxml.org"> #> [1] <phylogeny rooted="true">\n <name>A phylogenetic tree</name>\n <descrip ...