jhpoelen/rotl

Interface to Open Tree of Life API

An R interface to TOL API

This is the bleedingly-Alpha developmental version of an R package wrapping the Open Tree of Life data APIs, which being developed as part of the NESCENT/OpenTree/Arbor hackathon.

Check out the sister repos for Python and Ruby.

##Installation

If you want to play with these functions you can, via devtools.

library(devtools)

install_github("fmichonneau/rotl")

##Examples

Our first goal has been to impliment low-level functions that wrap the Open Tree APIs and return the complete response. These are now done (though we still need more tests and documentation), so we will shift our focus on developing higher level functions that automate common use cases and provide the results in the most approriate R object (often trees).

If you want to get started with open tree the existing functions can be used. Note: it's quite possible that function names or behaviours will change, so treat these as something to play with for now:

###Find trees focused on my favourite taxon

furry_studies <- studies_find_studies(property="ot:focalCladeOTTTaxonName", value="Mammalia")
> ( furry_ids <- unlist(furry_list$matched_studies) )
    ##ot:studyId ot:studyId ot:studyId ot:studyId ot:studyId 
    ##  "2647"     "1428"     "2582"     "2550"     "2812" 

###Get a tree into memory

First, use the studies_metadata to find the tree ID, then fetch a tree

furry_metadata <- httr::content(get_study_meta(2647))
furry_metadata$nexml$treesById
    ##$trees2647
    ##$trees2647$treeById
    ##$trees2647$treeById$tree6169
    ##NULL
    ##
    ##
    ##$trees2647$`^ot:treeElementOrder`
    ##$trees2647$`^ot:treeElementOrder`[[1]]
    ##[1] "tree6169"
    ##
    ##
    ##$trees2647$`@otus`
    ##[1] "otus2647"
    ##
tr_string <- get_study_tree(study="2647", tree="tree6169",format="newick")

library(ape)
tr <- read.tree(text=httr::content(tr_string))
plot(tr)

Get a subtree from the Big Tree

( some_birds <- tol_induced_subtree(ott_ids=c(292466, 501678, 267845, 666104)))
    #Response [http://devapi.opentreeoflife.org/v2/tree_of_life/induced_subtree]
    #  Status: 200
    #  Content-type: application/json; charset=UTF-8
    #{
    #  "subtree" : "((Stellula_ott501678,(Dendroica_ott666104,Cinclus_ott267845))Neognathae_ott241846,Struthio_ott292466)Aves_ott81461;",
    #  "ott_ids_not_in_tree" : [ ],
    #  "ott_ids_not_in_graph" : [ ],
    #  "node_ids_not_in_graph" : [ ],
    #  "node_ids_not_in_tree" : [ ]
    #} 
library(ape)
( tr <- read.tree(text=httr::content(some_birds)$subtree) )
    #
    #Phylogenetic tree with 4 tips and 3 internal nodes.
    #
    #Tip labels:
    #[1] "Stellula_ott501678"  "Dendroica_ott666104" "Cinclus_ott267845"  
    #[4] "Struthio_ott292466" 
    #Node labels:
    #[1] "Aves_ott81461"        "Neognathae_ott241846" ""                    
    #
    #Rooted; no branch lengths.