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)

Arguments¶

graph

An igraph graph object.

Value¶

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

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¶

### 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)