R: Convert a tree in ape 'phylo' format to igraph 'graph'...

phyloToGraph {alakazam} | R Documentation

## Convert a tree in ape `phylo` format to igraph `graph` format.

### Description

`phyloToGraph` converts a tree in `phylo` format to and `graph` format.

### Usage

    phyloToGraph(phylo, germline = NULL)

### Arguments

`phylo` | An ape `phylo` object.
`germline` | If specified, places specified tip sequence as the direct ancestor of the tree

### Details

Convert from phylo to graph object. Uses the node.label vector to label internal nodes. Nodes may rotate but overall topology will remain constant.

### Value

A `graph` object representing the input tree.

### References

1. Hoehn KB, Lunter G, Pybus OG - A Phylogenetic Codon Substitution Model for Antibody Lineages. Genetics 2017 206(1):417-427 https://doi.org/10.1534/genetics.116.196303

2. Hoehn KB, Vander Heiden JA, Zhou JQ, Lunter G, Pybus OG, Kleinstein SHK - Repertoire-wide phylogenetic models of B cell molecular evolution reveal evolutionary signatures of aging and vaccination. bioRxiv 2019 https://doi.org/10.1101/558825

### Examples

    ## Not run:
       library(igraph)
       library(ape)

       #convert to phylo
       phylo = graphToPhylo(graph)

       #plot tree using ape
       plot(phylo,show.node.label=TRUE)

       #store as newick tree
       write.tree(phylo,file="tree.newick")

       #read in tree from newick file
       phylo_r = read.tree("tree.newick")

       #convert to igraph
       graph_r = phyloToGraph(phylo_r,germline="Germline")

       #plot graph - same as before, possibly rotated
       plot(graph_r,layout=layout_as_tree)

    ## End(Not run)

[Package alakazam version 0.3.0 Index]