phylo2vec.utils.vector.get_node_depth

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phylo2vec.utils.vector.get_node_depth#

phylo2vec.utils.vector.get_node_depth(vector_or_matrix, node: int) → float[source]#

Get the depth of a node in a Phylo2Vec tree.

The depth of a node is the length of the path from the root to that node (i.e., distance from root). This follows the BEAST/ETE convention.

The root has depth 0, and depths increase as you move toward the leaves.

For vectors, topological depth is returned (all branch lengths = 1). For matrices, actual branch lengths are used.

Parameters:

  • vector_or_matrix (numpy.ndarray) – Phylo2Vec vector (ndim == 1) or matrix (ndim == 2)

  • node (int) – A node in the tree (0 to 2*n_leaves - 2)

Returns:

Depth of the node (distance from root)

Return type:

float

Examples

>>> import numpy as np
>>> from phylo2vec.utils.vector import get_node_depth
>>> # Tree: (0,(1,(2,3)4)5)6
>>> v = np.array([0, 1, 2])
>>> get_node_depth(v, 6)  # Root has depth 0
0.0
>>> get_node_depth(v, 0)  # Leaf 0 is 1 edge from root
1.0
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