phyloToGraph - 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

Value

A graph object representing the input 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.

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)