consensus_taxonomies: Compute consensus taxonomies across a tree.

In castor: Efficient Phylogenetics on Large Trees

Compute consensus taxonomies across a tree.

Description

Given a rooted phylogenetic tree and taxonomies for all tips, compute corresponding consensus taxonomies for all nodes in the tree based on their descending tips. The consensus taxonomy of a given node is the longest possible taxonomic path (i.e., to the lowest possible level) such that the taxonomies of all descending tips are nested within that taxonomic path. Some tip taxonomies may be incomplete, i.e., truncated at higher taxonomic levels. In that case, consensus taxonomy building will be conservative, i.e., no assumptions will be made about the missing taxonomic levels.

Usage

consensus_taxonomies(tree, tip_taxonomies = NULL, delimiter = ";")

Arguments

tree	A rooted tree of class "phylo".
tip_taxonomies	Optional, character vector of length Ntips, listing taxonomic paths for the tips. If NULL, then tip labels in the tree are assumed to be tip taxonomies.
delimiter	Character, the delimiter between taxonomic levels (e.g., ";" for SILVA and Greengenes taxonomies).

Details

Examples:

• If the descending tips of a node have taxonomies "A;B;C" and "A;B;C;D" and "A;B;C;E", then their consensus taxonomy is "A;B;C".

• If the descending tips of a node have taxonomies "A;B" and "A;B;C;D" and "A;B;C;E", then their consensus taxonomy is "A;B".

• If the descending tips of a node have taxonomies "X;B;C" and "Y;B;C", then their consensus taxonomy is "" (i.e., empty).

Value

A character vector of length Nnodes, listing the inferred consensus taxonomies for all nodes in the tree.

Author(s)

Stilianos Louca

Examples

# generate a random tree
tree = generate_random_tree(list(birth_rate_factor=0.1), max_tips=7)$tree

# define a character vector storing hypothetical tip taxonomies
tip_taxonomies = c("R;BB;C", "AA;BB;C;DD", "AA;BB;C;E", 
                   "AA;BB", "AA;BB;D", "AA;BB;C;F", "AA;BB;C;X")

# compute consensus taxonomies and store them in the tree as node labels
tree$node.label = castor::consensus_taxonomies(tree, 
                                               tip_taxonomies = tip_taxonomies, 
                                               delimiter = ";")

castor documentation built on Aug. 18, 2023, 1:07 a.m.