alakazam (version 1.3.0)

graphToPhylo: 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)

Value

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

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.

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

if (FALSE) {
   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)
}