In DessimozLab/OmaDB: R wrapper for the OMA REST API

Using OmaDB, a user can easily obtain a taxonomic tree of interest using the getTaxonomy structure. The tree can be restricted to a certain root or by a list of members and the data is returned in the newick format. The newick can then be exported and used to create a tree object using ape which can then be visualised using ggtree.

This is done below using the getTaxonomy(root='Alveolata') function, the output of which is below.

library(OmaDB)

load('../data/taxonomy.rda')

getObjectAttributes(taxonomy)

The tree can be further analysed and annotated using the ggtree package also available in Bioconductor. This can easily be done using the getTree() function in OmaDB.

DessimozLab/OmaDB documentation built on April 19, 2024, 9:54 p.m.