In klarakaleb/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.
klarakaleb/OmaDB documentation built on April 18, 2024, 8:03 a.m.
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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.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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