phylostructure: Generating Node Relations
In yunfantang/PhyloScan: Phylogenetic Scan Test for Microbiome Data

Description Usage Arguments Details Value Author(s) Examples

View source: R/phylostructure.R

phylostructure returns the neighboring nodes and descendant leaves for each internal node of a binary phylogenetic tree.

1	phylostructure(phylotree)

phylotree

A phylo-class object as in the phyloseq package. The tree has to be binary.

For each internal node (i.e. non-leaf node) in phylotree, this function calculates its parent node, child nodes and all of its descendant leaves. The labeling of nodes are the same as in phylotree$edge, which is assumed to obey the following convention. Leaves are labeled from 1 to ntaxa(phylotree) and internal nodes are labeled from ntaxa(phylotree) + 1 to ntaxa(phylotree) + phylotree$Nnode. The root label is ntaxa(phylotree) + 1. Parent node always has a lower label than its child internal nodes.

A list containing the following components:

`phylotree`	Input object
`phylochildren`	Numerical matrix of child node labels. The kth row contains the children node labels of node k. Leaf nodes have their their row vectors set to zero.
`phyloparent`	Numerical vector of parent node labels. The kth element contains the parent node label of node k. Root node has its parent set to zero.
`descendant`	Logical matrix of decendant leaves. The kth row shows whether the leaves are descendants of node k.

Yunfan Tang

library(ape)
set.seed(10)

## Analyze a random binary phylogenetic tree with 6 leaf nodes
pstrct <- phylostructure(rtree(6))
## Show children of node 7 (root):
pstrct$phylochildren[7, ]
## Show parent of node 1:
pstrct$phyloparent[1]
## List all leaf nodes under node 8:
which(pstrct$descendant[8, ])