getPathLengths - Calculate path lengths from the tree root

Description

getPathLengths calculates the unweighted (number of steps) and weighted (distance) path lengths from the root of a lineage tree.

Usage

getPathLengths(graph, root = "Germline", field = NULL, exclude = NULL)

Arguments

graph
igraph object containing an annotated lineage tree.
root
name of the root (germline) node.
field
annotation field to use for exclusion of nodes from step count.
exclude
annotation values specifying which nodes to exclude from step count. If NULL consider all nodes. This does not affect the weighted (distance) path length calculation.

Value

A data.frame with columns:

  • name: node name
  • steps: path length as the number of nodes traversed
  • distance: path length as the sum of edge weights

Examples

# Define example graph
graph <- ExampleTrees[[24]]

# Consider all nodes
getPathLengths(graph, root="Germline")


            name steps distance
1      Inferred1     1       20
2 GN5SHBT04CW57C     2       26
3      Inferred2     3       28
4 GN5SHBT08I7RKL     4       29
5 GN5SHBT04CAVIG     5       30
6       Germline     0        0
7 GN5SHBT01D6X0W     2       22
8 GN5SHBT06H7TQD     6       31
9 GN5SHBT05HEG2J     4       33



# Exclude nodes without an isotype annotation from step count
getPathLengths(graph, root="Germline", field="c_call", exclude=NA)

            name steps distance
1      Inferred1     0       20
2 GN5SHBT04CW57C     1       26
3      Inferred2     1       28
4 GN5SHBT08I7RKL     2       29
5 GN5SHBT04CAVIG     3       30
6       Germline     0        0
7 GN5SHBT01D6X0W     1       22
8 GN5SHBT06H7TQD     4       31
9 GN5SHBT05HEG2J     2       33

See also

See buildPhylipLineage for generating input trees.