summarizeSubtrees - 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.
Examples¶
# Summarize a tree
graph <- ExampleTrees[[23]]
summarizeSubtrees(graph, fields="c_call", root="Germline")
name c_call parent outdegree size depth pathlength outdegree_norm size_norm depth_norm pathlength_norm
1 GN5SHBT06HH3QD IGHA Germline 1 6 3 10 0.1666667 0.8571429 0.75 0.3333333
2 GN5SHBT08F45HV IGHA,IGHG GN5SHBT06HH3QD 4 5 2 7 0.6666667 0.7142857 0.50 0.2333333
3 Germline <NA> <NA> 1 7 4 30 0.1666667 1.0000000 1.00 1.0000000
4 GN5SHBT06IFV0R IGHG GN5SHBT08F45HV 0 1 1 0 0.0000000 0.1428571 0.25 0.0000000
5 GN5SHBT08I3P11 IGHG GN5SHBT08F45HV 0 1 1 0 0.0000000 0.1428571 0.25 0.0000000
6 GN5SHBT01BXJY7 IGHG GN5SHBT08F45HV 0 1 1 0 0.0000000 0.1428571 0.25 0.0000000
7 GN5SHBT01EGEU6 IGHA GN5SHBT08F45HV 0 1 1 0 0.0000000 0.1428571 0.25 0.0000000
See also¶
See buildPhylipLineage for generating input trees. See getPathLengths for calculating path length to nodes.