Source code for kmapper.nerve

import itertools
from collections import defaultdict

__all__ = ["GraphNerve"]

class Nerve:
    """Base class for implementations of a nerve finder to build a Mapper complex."""

    def __init__(self):

    def compute(self, nodes, links):
        raise NotImplementedError()

[docs]class GraphNerve(Nerve): """Creates the 1-skeleton of the Mapper complex. Parameters ----------- min_intersection: int, default is 1 Minimum intersection considered when computing the nerve. An edge will be created only when the intersection between two nodes is greater than or equal to `min_intersection` """
[docs] def __init__(self, min_intersection=1): self.min_intersection = min_intersection
def __repr__(self): return "GraphNerve(min_intersection={})".format(self.min_intersection)
[docs] def compute(self, nodes): """Helper function to find edges of the overlapping clusters. Parameters ---------- nodes: A dictionary with entires `{node id}:{list of ids in node}` Returns ------- edges: A 1-skeleton of the nerve (intersecting nodes) simplicies: Complete list of simplices """ result = defaultdict(list) # Create links when clusters from different hypercubes have members with the same sample id. candidates = itertools.combinations(nodes.keys(), 2) for candidate in candidates: # if there are non-unique members in the union if ( len(set(nodes[candidate[0]]).intersection(nodes[candidate[1]])) >= self.min_intersection ): result[candidate[0]].append(candidate[1]) edges = [[x, end] for x in result for end in result[x]] simplices = [[n] for n in nodes] + edges return result, simplices
class SimplicialNerve(Nerve): """Creates the entire Cech complex of the covering defined by the nodes. Warning: Not implemented yet. """ def compute(self, nodes, links=None): pass