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 ...