rphyloxml

rphyloxml provides access to the phyloXML file format. For now, the only functions that are implemented in the package are:

write_phyloxml: A method to coerce phylo objects from the ape package as phyloXML (XML) documents.
read_phyloxml: A method to read phyloXML documents into R. It returns a data frame with the structure of the tree and a nested list with each nodes’ annotations.
validate_phyloxml: A wrapper of xml2::xml_validate, which allows validating a phyloXML doc using the phyloxml.xsd schema (see here)

This package has been motivated to be used with the javascript library jsPhyloSVG, for which we are currently developing an R package with the same name that provides an htmlwidget here.

Installation

You can install rphyloxml from github with:

# install.packages("devtools")
devtools::install_github("USCBiostats/rphyloxml")

Writing phyloXML files

In the following example, we create a random tree using the rtree function from the ape package, and later on coerce it into a phyloXML document using write_phyloxml.

library(ape)
library(rphyloxml)
set.seed(12)

x <- rtree(3)
x
#> 
#> Phylogenetic tree with 3 tips and 2 internal nodes.
#> 
#> Tip labels:
#> [1] "t2" "t3" "t1"
#> 
#> Rooted; includes branch lengths.

z <- write_phyloxml(x)
z
#> {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" rerootable="false">\n    <name>A phylogenetic tr ...

You can get a “nicer” view of it by doing the following:

cat(as.character(z))
#> <?xml version="1.0" encoding="UTF-8"?>
#> <phyloxml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://www.phyloxml.org" xsi:schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd">
#>   <phylogeny rooted="true" rerootable="false">
#>     <name>A phylogenetic tree</name>
#>     <description>Some description</description>
#>     <clade>
#>       <clade>
#>         <branch_length>0.26938187633641064167</branch_length>
#>         <clade>
#>           <name>t2</name>
#>           <branch_length>0.16934812325052917004</branch_length>
#>         </clade>
#>         <clade>
#>           <name>t3</name>
#>           <branch_length>0.03389562247321009636</branch_length>
#>         </clade>
#>       </clade>
#>       <clade>
#>         <name>t1</name>
#>         <branch_length>0.17878500418737530708</branch_length>
#>       </clade>
#>     </clade>
#>   </phylogeny>
#> </phyloxml>

And to store the document, you just need to use xml2 (which is what powers the package) as follows:

xml2::write_xml(z, "mynicetree.xml")

Reading XML files

We will read the file amphibian_tree_of_life_Frost_DR_2006.xml available in both the package and the phyloxml website.

# Reading from the package files
fn <- system.file("phyloxml/amphibian_tree_of_life_Frost_DR_2006.xml", package="rphyloxml")
xmltree <- read_phyloxml(fn)

str(xmltree, 4)
#> List of 1
#>  $ Amphibian Phylogeny, Frost DR, 2006:List of 4
#>   ..$ .Data     :'data.frame':   715 obs. of  4 variables:
#>   .. ..$ id           : int [1:715] 359 360 361 362 363 364 365 366 367 368 ...
#>   .. ..$ isleaf       : logi [1:715] FALSE FALSE FALSE FALSE FALSE FALSE ...
#>   .. ..$ parent       : int [1:715] NA 359 360 361 362 363 364 365 366 367 ...
#>   .. ..$ branch_length: logi [1:715] NA NA NA NA NA NA ...
#>   ..$ node.meta :List of 715
#>   .. ..$ :List of 1
#>   .. .. ..$ taxonomy:List of 2
#>   .. ..$ : Named list()
#>   .. ..$ :List of 1
#>   .. .. ..$ taxonomy:List of 3
#>   .. ..$ :List of 1
#>   .. .. ..$ taxonomy:List of 3
#>   .. ..$ :List of 1
#>   .. .. ..$ taxonomy:List of 3
#>   .. ..$ : Named list()
#>   .. ..$ : Named list()
#>   .. ..$ : Named list()
#>   .. ..$ :List of 1
#>   .. .. ..$ taxonomy:List of 3
#>   .. ..$ : Named list()
#>   .. ..$ : Named list()
#>   .. ..$ : Named list()
#>   .. ..$ :List of 1
#>   .. .. ..$ taxonomy:List of 3
#>   .. ..$ : Named list()
#>   .. ..$ : Named list()
#>   .. ..$ : Named list()
#>   .. ..$ : Named list()
#>   .. ..$ : Named list()
#>   .. ..$ : Named list()
#>   .. ..$ : Named list()
#>   .. ..$ : Named list()
#>   .. ..$ :List of 2
#>   .. .. ..$ color   :List of 3
#>   .. .. ..$ taxonomy:List of 4
#>   .. ..$ :List of 1
#>   .. .. ..$ color:List of 3
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#>   .. .. ..$ taxonomy:List of 6
#>   .. ..$ :List of 1
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#>   .. .. ..$ taxonomy:List of 5
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#>   .. .. ..$ color   :List of 3
#>   .. .. ..$ taxonomy:List of 3
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#>   .. .. ..$ color:List of 3
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#>   .. .. ..$ color:List of 3
#>   .. ..$ :List of 1
#>   .. .. ..$ color:List of 3
#>   .. ..$ :List of 2
#>   .. .. ..$ color   :List of 3
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#>   .. .. ..$ color   :List of 3
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#>   .. .. ..$ taxonomy:List of 3
#>   .. ..$ :List of 1
#>   .. .. ..$ color:List of 3
#>   .. ..$ :List of 2
#>   .. .. ..$ color   :List of 3
#>   .. .. ..$ taxonomy:List of 3
#>   .. ..$ :List of 2
#>   .. .. ..$ color   :List of 3
#>   .. .. ..$ taxonomy:List of 4
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#>   .. ..$ :List of 2
#>   .. .. ..$ color   :List of 3
#>   .. .. ..$ taxonomy:List of 3
#>   .. ..$ :List of 1
#>   .. .. ..$ color:List of 3
#>   .. ..$ :List of 2
#>   .. .. ..$ color   :List of 3
#>   .. .. ..$ taxonomy:List of 4
#>   .. ..$ :List of 2
#>   .. .. ..$ color   :List of 3
#>   .. .. ..$ taxonomy:List of 3
#>   .. ..$ :List of 2
#>   .. .. ..$ color   :List of 3
#>   .. .. ..$ taxonomy:List of 5
#>   .. .. [list output truncated]
#>   ..$ rooted    : chr "true"
#>   ..$ rerootable: chr "false"
#>  - attr(*, "class")= chr "phyloxml"

# We can coerce this into a mulitphylo list
(apetree <- phyloxml2phylo(xmltree))[[1]]
#> 
#> Phylogenetic tree with 358 tips and 357 internal nodes.
#> 
#> Tip labels:
#>  =119767|Capensibufo rosei, =125255|Capensibufo tradouwi, =119769|Stephopaedes anotis, =8386|Bufo marinus, =8384|Bufo bufo, =103606|Torrentophryne aspinia, ...
#> 
#> Rooted; includes branch lengths.

plot(apetree, cex=.25)
#> Warning in plot.phylo(x[[i]], ...): 715 branch length(s) NA(s): branch lengths
#> ignored in the plot

Name		Name	Last commit message	Last commit date
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R		R
docs		docs
inst		inst
man		man
playground		playground
tests		tests
.Rbuildignore		.Rbuildignore
.gitignore		.gitignore
.travis.yml		.travis.yml
ChangeLog		ChangeLog
DESCRIPTION		DESCRIPTION
LICENSE		LICENSE
LICENSE.md		LICENSE.md
NAMESPACE		NAMESPACE
README.Rmd		README.Rmd
README.md		README.md
appveyor.yml		appveyor.yml
codecov.yml		codecov.yml
rphyloxml.Rproj		rphyloxml.Rproj
structure.md		structure.md

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rphyloxml

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Writing phyloXML files

Reading XML files

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