python - 如何从邻接矩阵仅针对特定节点创建网络图？

Question

我有一个邻接矩阵 5000X5000，我想创建一个网络图。要求是用户输入节点，输出将是该特定输入节点的图形(第一和第二度)。

我已经尝试过使用 Gephi，但由于邻接矩阵很大，我无法专注于每个节点。所以我想是否可以为特定节点创建一个图(因为我只对每个节点的第一和第二度连接感兴趣，而不是超出这个范围)

Gephi 是基于 UI 的，所以我没有代码。

输入将是一个node_id，输出将是与该node_id对应的图(第一和第二度连接)

Answer 1

这是使用 networkx 的实现:

import networkx as nx
import numpy as np

# make dummy adjacency matrix
a = np.random.rand(100,100)
a = np.tril(a)
a = a>0.95

# make graph from adjaceny matrix
G = nx.from_numpy_matrix(a)


def neigh(G, node, depth):
    """ given starting node, recursively find neighbours
        until desired depth is reached
    """

    node_list = []
    if depth==0:
        node_list.append(node)
    else:
        for neighbor in G.neighbors(node):
            node_list.append(node)
            node_list += neigh(G, neighbor, depth-1)
    return list(set(node_list)) # intermediate conversion to set to lose duplicates. 

# a bit more compressed:
def neigh_short(G, node, depth):
    """ given starting node, recursively find neighbours
        until desired depth is reached
    """

    node_list = [node]
    if depth>0:
        for neighbor in G.neighbors(node)
            node_list += neigh_short(G, neighbor, depth-1)
    return list(set(node_list)) # intermediate conversion to set to lose duplicates. 

# example:
# find all neighbours with distance 2 from node 5:
n = neigh(G, node=5, depth=2)

# extract the respective subgraph from G and store in H
H = G.subgraph(n)