summarizeSubtrees {alakazam} | R Documentation |
summarizeSubtrees
calculates summary statistics for each node of a tree. Includes
both node properties and subtree properties.
summarizeSubtrees(graph, fields = NULL, root = "Germline")
graph |
igraph object containing an annotated lineage tree. |
fields |
annotation fields to add to the output. |
root |
name of the root (germline) node. |
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 buildPhylipLineage for generating input trees. See getPathLengths for calculating path length to nodes.
# Summarize a tree
graph <- ExampleTrees[[23]]
summarizeSubtrees(graph, fields="c_call", root="Germline")