getTaxonomy: Get the Taxonomic tree function
In OmaDB: R wrapper for the OMA REST API
Description
Usage
Arguments
Value
Examples
Description
The function to obtain the taxonomic tree from the database in the newick format that can be plugged into phylo.io for visualisation.
Usage
1
getTaxonomy(root = NULL, members = NULL, newick = TRUE)
Arguments
root
optional parameter, the root of the node of interest
members
optional parameter, list of member ncbi taxon or UniProt IDs that should be included in the induced taxonomy.
newick
optional parameter, boolean default set to TRUE
Value
an object containing the JSON keys as attributes
Examples
1
2
3
getTaxonomy()
getTaxonomy(members='YEAST,ASHGO')
getTaxonomy(root='Alveolata')
OmaDB documentation built on Nov. 13, 2020, 2 a.m.
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Description Usage Arguments Value Examples
Description
The function to obtain the taxonomic tree from the database in the newick format that can be plugged into phylo.io for visualisation.
Usage
1 | getTaxonomy(root = NULL, members = NULL, newick = TRUE)
|
Arguments
root |
optional parameter, the root of the node of interest |
members |
optional parameter, list of member ncbi taxon or UniProt IDs that should be included in the induced taxonomy. |
newick |
optional parameter, boolean default set to TRUE |
Value
an object containing the JSON keys as attributes
Examples
1 2 3 | getTaxonomy()
getTaxonomy(members='YEAST,ASHGO')
getTaxonomy(root='Alveolata')
|
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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