summarizeSubtrees {alakazam}  R Documentation 
Generate subtree summary statistics for a tree
Description
summarizeSubtrees
calculates summary statistics for each node of a tree. Includes
both node properties and subtree properties.
Usage
summarizeSubtrees(graph, fields = NULL, root = "Germline")
Arguments
graph 
igraph object containing an annotated lineage tree. 
fields 
annotation fields to add to the output. 
root 
name of the root (germline) node. 
Value
A data.frame with columns:

name
: node name. 
parent
: name of the parent node. 
outdegree
: number of edges leading from the node. 
size
: total number of nodes within the subtree rooted at the node. 
depth
: the depth of the subtree that is rooted at the node. 
pathlength
: the maximum pathlength beneath the node. 
outdegree_norm
:outdegree
normalized by the total number of edges. 
size_norm
:size
normalized by the largest subtree size (the germline). 
depth_norm
:depth
normalized by the largest subtree depth (the germline). 
pathlength_norm
:pathlength
normalized by the largest subtree pathlength (the germline).
An additional column corresponding to the value of field
is added when
specified.
See Also
See buildPhylipLineage for generating input trees. See getPathLengths for calculating path length to nodes.
Examples
# Summarize a tree
graph < ExampleTrees[[23]]
summarizeSubtrees(graph, fields="c_call", root="Germline")