getPathLengths: Calculate path lengths from the tree root

In alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis

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

See Also

See buildPhylipLineage for generating input trees.

Examples

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

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

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

alakazam documentation built on Sept. 30, 2023, 9:07 a.m.