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

In alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis

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 = "Germline")

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)

alakazam documentation built on Sept. 30, 2023, 9:07 a.m.