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
1 GN5SHBT06HH3QD      IGHA       Germline         1    6     3         10
2 GN5SHBT08F45HV IGHA,IGHG GN5SHBT06HH3QD         4    5     2          7
3       Germline      <NA>           <NA>         1    7     4         30
4 GN5SHBT06IFV0R      IGHG GN5SHBT08F45HV         0    1     1          0
5 GN5SHBT08I3P11      IGHG GN5SHBT08F45HV         0    1     1          0
6 GN5SHBT01BXJY7      IGHG GN5SHBT08F45HV         0    1     1          0
7 GN5SHBT01EGEU6      IGHA GN5SHBT08F45HV         0    1     1          0
  outdegree_norm size_norm depth_norm pathlength_norm
1      0.1666667 0.8571429       0.75       0.3333333
2      0.6666667 0.7142857       0.50       0.2333333
3      0.1666667 1.0000000       1.00       1.0000000
4      0.0000000 0.1428571       0.25       0.0000000
5      0.0000000 0.1428571       0.25       0.0000000
6      0.0000000 0.1428571       0.25       0.0000000
7      0.0000000 0.1428571       0.25       0.0000000

See also

See buildPhylipLineage for generating input trees. See getPathLengths for calculating path length to nodes.