| getPathLengths {alakazam} | R Documentation |
getPathLengths calculates the unweighted (number of steps) and weighted (distance)
path lengths from the root of a lineage tree.
getPathLengths(graph, root = "Germline", field = NULL, exclude = NULL)
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 |
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 buildPhylipLineage for generating input trees.
# 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="ISOTYPE", exclude=NA)