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rphyloxml's Introduction

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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
#>   .. ..$ :List of 1
#>   .. .. ..$ color:List of 3
#>   .. ..$ :List of 1
#>   .. .. ..$ color:List of 3
#>   .. ..$ :List of 1
#>   .. .. ..$ color:List of 3
#>   .. ..$ :List of 1
#>   .. .. ..$ color:List of 3
#>   .. ..$ :List of 1
#>   .. .. ..$ color: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 3
#>   .. ..$ :List of 2
#>   .. .. ..$ color   :List of 3
#>   .. .. ..$ taxonomy:List of 3
#>   .. ..$ :List of 2
#>   .. .. ..$ color   :List of 3
#>   .. .. ..$ taxonomy:List of 4
#>   .. ..$ :List of 2
#>   .. .. ..$ color   :List of 3
#>   .. .. ..$ taxonomy:List of 6
#>   .. ..$ :List of 1
#>   .. .. ..$ color:List of 3
#>   .. ..$ :List of 2
#>   .. .. ..$ color   :List of 3
#>   .. .. ..$ taxonomy:List of 5
#>   .. ..$ :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 5
#>   .. ..$ :List of 2
#>   .. .. ..$ color   :List of 3
#>   .. .. ..$ taxonomy:List of 3
#>   .. ..$ :List of 1
#>   .. .. ..$ color:List of 3
#>   .. ..$ :List of 1
#>   .. .. ..$ color: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 3
#>   .. ..$ :List of 2
#>   .. .. ..$ color   :List of 3
#>   .. .. ..$ taxonomy:List of 4
#>   .. ..$ :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 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
#>   .. ..$ :List of 1
#>   .. .. ..$ color:List of 3
#>   .. ..$ :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 4
#>   .. ..$ :List of 2
#>   .. .. ..$ color   :List of 3
#>   .. .. ..$ taxonomy:List of 4
#>   .. ..$ :List of 2
#>   .. .. ..$ color   :List of 3
#>   .. .. ..$ taxonomy:List of 5
#>   .. ..$ :List of 2
#>   .. .. ..$ color   :List of 3
#>   .. .. ..$ taxonomy:List of 3
#>   .. ..$ : Named list()
#>   .. ..$ :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 of 2
#>   .. .. ..$ color   :List of 3
#>   .. .. ..$ taxonomy:List of 3
#>   .. ..$ :List of 2
#>   .. .. ..$ color   :List of 3
#>   .. .. ..$ taxonomy:List of 3
#>   .. ..$ :List of 2
#>   .. .. ..$ color   :List of 3
#>   .. .. ..$ taxonomy:List of 6
#>   .. ..$ :List of 2
#>   .. .. ..$ color   :List of 3
#>   .. .. ..$ taxonomy:List of 6
#>   .. ..$ :List of 2
#>   .. .. ..$ color   :List of 3
#>   .. .. ..$ taxonomy:List of 4
#>   .. ..$ : Named list()
#>   .. ..$ : Named list()
#>   .. ..$ : Named list()
#>   .. ..$ : Named list()
#>   .. ..$ :List of 2
#>   .. .. ..$ color   :List of 3
#>   .. .. ..$ taxonomy:List of 3
#>   .. ..$ :List of 2
#>   .. .. ..$ color   :List of 3
#>   .. .. ..$ taxonomy:List of 3
#>   .. ..$ :List of 2
#>   .. .. ..$ color   :List of 3
#>   .. .. ..$ taxonomy: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
#>   .. ..$ :List of 2
#>   .. .. ..$ color   :List of 3
#>   .. .. ..$ taxonomy:List of 4
#>   .. ..$ :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 4
#>   .. ..$ :List of 2
#>   .. .. ..$ color   :List of 3
#>   .. .. ..$ taxonomy:List of 4
#>   .. ..$ : Named list()
#>   .. ..$ :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 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 4
#>   .. ..$ :List of 2
#>   .. .. ..$ color   :List of 3
#>   .. .. ..$ taxonomy:List of 4
#>   .. ..$ : Named list()
#>   .. ..$ : Named list()
#>   .. ..$ :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

rphyloxml's People

Contributors

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Watchers

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rphyloxml's Issues

function "read_phyloxml" returned a zero-length list

I am trying to read phylogenetic trees from XML files by function "read_phyloxml", but it returns a list with zero length. I tried with my own XML tree downloaded from Tree of Life, and I also ran the example code of the package instructions, but the same problem happened: it returned List of 0.
Here is the code. The file "test.xml" I use is accessible in http://tolweb.org/onlinecontributors/appservice=external&page=xml/TreeStructureService&node_id=8205).

`####### my insect phylogenetic trees
library(rphyloxml)
phyloinsect <- read_phyloxml ("C://Users/Hanlun Liu/Desktop/plphylogeny/test.xml")
str(phyloinsect)

####### examples from github
fn <- system.file("phyloxml/amphibian_tree_of_life_Frost_DR_2006.xml", package="rphyloxml")
xmltree <- read_phyloxml(fn)
str(xmltree)
read_phyloxml("amphibian_tree_of_life_Frost_DR_2006.xml")

######## examples from R help
library(ape)
set.seed(1)
x <- rtree(10)
x2 <- write_phyloxml(x)
a <- read_phyloxml(x2)
str(a)`

all str() return Named list() - attr(*, "class")= chr "phyloxml"

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