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

graphToPhylo {alakazam} | R Documentation

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

### Description

`graphToPhylo` a tree in igraph `graph` format to ape `phylo` format.

### Usage

    graphToPhylo(graph)

### Arguments

`graph` | An igraph `graph` object.

### Details

Convert from igraph `graph` object to ape `phylo` object. If `graph` object was previously rooted with the germline as the direct ancestor, this will re-attach the germline as a descendant node with a zero branch length to a new universal common ancestor (UCA) node and store the germline node ID in the `germid` attribute and UCA node number in the `uca` attribute. Otherwise these attributes will not be specified in the `phylo` object. Using `phyloToGraph(phylo, germline=phylo$germid)` creates a `graph` object with the germline back as the direct ancestor. Tip and internal node names are stored in the `tip.label` and `node.label` vectors, respectively.

### Value

A `phylo` object representing the input tree. Tip and internal node names are stored in the `tip.label` and `node.label` vectors, respectively.

### 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]