如何使用鼠标手动放置 networkx 节点?

问题描述

我有一个相当大且杂乱的节点网络，我希望尽可能整齐地显示它.

I have a fairly large and messy network of nodes that I wish to display as neatly as possible.

这是它当前的显示方式:

This is how it's currently being displayed:

首先，我尝试使用布局来查看它是否可以自动生成良好的输出.

First, I tried playing with the layout to see if it could generate a good output automatically.

我尝试了许多不同的 nx 布局，但它们都显示了相似的结果.我还尝试了所有这些堆栈交换问题的答案:

I have tried many different nx layouts, but they all display similar results. I have also tried answers from all of these stack exchange questions:

如何增加 networkx.spring_layout 的节点间距

使用 networkX 和 matplotlib 绘制巨大的图形

NetworkX - 阻止节点聚集 - 尝试尺度/K参数

在 NetworkX spring 中修复节点子集的位置图

这是我使用的代码:

import networkx as nx
import matplotlib.pyplot as plt\

def generate_plot(connections, filename):

    G=nx.Graph()
    G.add_edges_from(connections)

    nx.draw(G)

    plt.show()
    #plt.savefig(filename)

这是我要显示的数据:

connections = [(0, 36), (0, 113), (2, 11), (2, 12), (2, 26), (2, 27), (2, 28), (2, 29), (2, 32), (2, 33), (2, 34), (2, 35), (2, 82), (3, 41), (4, 41), (5, 3), (6, 3), (11, 7), (11, 10), (11, 13), (11, 42), (12, 10), (12, 164), (26, 10), (26, 100), (27, 10), (27, 164), (28, 10), (28, 92), (29, 56), (29, 58), (29, 79), (29, 91), (29, 99), (29, 100), (29, 101), (29, 102), (30, 59), (30, 83), (30, 99), (31, 55), (31, 56), (31, 57), (31, 74), (31, 91), (31, 96), (31, 100), (31, 113), (31, 134), (31, 164), (32, 10), (33, 10), (34, 10), (34, 164), (35, 10), (35, 91), (35, 100), (36, 64), (36, 74), (36, 82), (36, 91), (36, 107), (36, 99), (38, 41), (39, 40), (39, 41), (39, 59), (40, 41), (40, 47), (40, 91), (40, 99), (41, 3), (41, 39), (41, 40), (43, 68), (43, 69), (45, 50), (46, 51), (46, 69), (46, 99), (47, 49), (47, 91), (47, 107), (47, 100), (47, 101), (47, 113), (48, 76), (50, 68), (50, 69), (51, 68), (51, 76), (51, 114), (52, 46), (52, 47), (52, 65), (53, 42), (53, 107), (53, 99), (53, 100), (53, 101), (53, 113), (54, 76), (55, 74), (55, 96), (55, 99), (56, 99), (56, 100), (56, 109), (57, 29), (57, 64), (57, 91), (57, 96), (57, 107), (57, 100), (58, 91), (58, 99), (58, 100), (58, 101), (58, 102), (59, 30), (59, 46), (59, 47), (59, 61), (59, 83), (59, 99), (59, 100), (59, 101), (60, 3), (60, 12), (60, 26), (60, 27), (60, 29), (60, 30), (60, 31), (60, 35), (60, 36), (60, 40), (60, 42), (60, 44), (60, 49), (60, 55), (60, 56), (60, 57), (60, 58), (60, 59), (60, 61), (60, 64), (60, 74), (60, 75), (60, 79), (60, 81), (60, 82), (60, 83), (60, 86), (60, 90), (60, 91), (60, 92), (60, 93), (60, 94), (60, 96), (60, 107), (60, 99), (60, 100), (60, 101), (60, 102), (60, 111), (60, 112), (60, 113), (60, 116), (60, 126), (60, 129), (60, 134), (60, 135), (60, 136), (60, 140), (60, 144), (60, 150), (60, 152), (60, 162), (60, 164), (60, 179), (60, 195), (61, 91), (61, 107), (61, 100), (61, 101), (61, 113), (61, 135), (62, 79), (62, 102), (63, 59), (64, 29), (64, 36), (64, 91), (64, 99), (64, 100), (64, 101), (64, 140), (65, 12), (65, 27), (65, 29), (65, 30), (65, 31), (65, 34), (65, 35), (65, 43), (65, 45), (65, 50), (65, 56), (65, 57), (65, 58), (65, 59), (65, 60), (65, 61), (65, 66), (65, 67), (65, 72), (65, 75), (65, 81), (65, 82), (65, 91), (65, 92), (65, 96), (65, 107), (65, 99), (65, 100), (65, 101), (65, 102), (65, 104), (65, 109), (65, 129), (65, 140), (65, 142), (65, 156), (65, 164), (67, 68), (67, 69), (67, 195), (68, 60), (69, 51), (69, 53), (69, 68), (69, 195), (70, 12), (70, 26), (70, 29), (70, 31), (70, 35), (70, 47), (70, 56), (70, 58), (70, 59), (70, 61), (70, 66), (70, 75), (70, 79), (70, 82), (70, 83), (70, 93), (70, 96), (70, 107), (70, 99), (70, 100), (70, 101), (70, 126), (70, 129), (70, 135), (70, 136), (70, 162), (70, 164), (71, 12), (71, 26), (71, 29), (71, 31), (71, 35), (71, 47), (71, 56), (71, 58), (71, 59), (71, 61), (71, 66), (71, 75), (71, 79), (71, 83), (71, 96), (71, 107), (71, 99), (71, 100), (71, 101), (71, 126), (71, 135), (71, 162), (71, 164), (72, 29), (72, 35), (72, 36), (72, 46), (72, 47), (72, 55), (72, 57), (72, 58), (72, 60), (72, 61), (72, 64), (72, 66), (72, 70), (72, 71), (72, 74), (72, 75), (72, 76), (72, 79), (72, 86), (72, 90), (72, 91), (72, 93), (72, 94), (72, 95), (72, 96), (72, 107), (72, 99), (72, 100), (72, 101), (72, 102), (72, 111), (72, 112), (72, 116), (72, 126), (72, 129), (72, 144), (73, 83), (74, 96), (74, 100), (75, 100), (76, 29), (76, 31), (76, 42), (76, 44), (76, 49), (76, 55), (76, 56), (76, 59), (76, 61), (76, 66), (76, 74), (76, 78), (76, 83), (76, 91), (76, 93), (76, 96), (76, 107), (76, 109), (76, 113), (76, 114), (76, 116), (76, 134), (76, 140), (77, 30), (77, 44), (77, 49), (77, 61), (77, 74), (77, 78), (77, 83), (77, 96), (77, 109), (77, 140), (78, 61), (78, 91), (78, 92), (79, 44), (79, 99), (80, 42), (80, 64), (80, 65), (80, 75), (80, 83), (80, 134), (80, 135), (80, 136), (80, 144), (80, 155), (81, 35), (81, 91), (81, 100), (82, 10), (83, 84), (83, 85), (83, 86), (83, 107), (83, 100), (84, 194), (84, 195), (87, 36), (87, 88), (87, 142), (87, 144), (88, 59), (88, 83), (88, 134), (88, 135), (88, 136), (88, 144), (88, 158), (88, 162), (89, 61), (89, 135), (89, 141), (90, 36), (91, 96), (91, 113), (93, 96), (93, 107), (93, 134), (93, 135), (94, 74), (94, 96), (95, 61), (95, 134), (95, 135), (95, 162), (96, 35), (96, 74), (96, 91), (96, 99), (96, 100), (96, 101), (98, 12), (98, 26), (98, 27), (98, 29), (98, 30), (98, 31), (98, 34), (98, 35), (98, 41), (98, 56), (98, 57), (98, 58), (98, 59), (98, 60), (98, 61), (98, 70), (98, 75), (98, 79), (98, 81), (98, 82), (98, 83), (98, 84), (98, 87), (98, 91), (98, 92), (98, 95), (98, 96), (98, 107), (98, 99), (98, 100), (98, 101), (98, 106), (98, 134), (98, 135), (98, 142), (98, 147), (98, 152), (98, 159), (99, 91), (99, 113), (99, 164), (100, 91), (100, 101), (100, 113), (100, 164), (101, 57), (101, 91), (101, 113), (101, 164), (102, 101), (103, 44), (103, 61), (103, 140), (104, 56), (104, 90), (104, 101), (104, 102), (104, 104), (104, 129), (104, 140), (105, 83), (105, 135), (106, 2), (106, 29), (106, 30), (106, 31), (106, 36), (106, 41), (106, 48), (106, 56), (106, 57), (106, 58), (106, 59), (106, 60), (106, 61), (106, 62), (106, 63), (106, 65), (106, 66), (106, 68), (106, 70), (106, 71), (106, 72), (106, 74), (106, 75), (106, 76), (106, 77), (106, 78), (106, 79), (106, 80), (106, 81), (106, 82), (106, 83), (106, 84), (106, 85), (106, 87), (106, 89), (106, 90), (106, 91), (106, 92), (106, 93), (106, 94), (106, 95), (106, 96), (106, 107), (106, 99), (106, 100), (106, 101), (106, 102), (106, 103), (106, 104), (106, 105), (106, 108), (106, 110), (106, 111), (106, 112), (106, 116), (106, 119), (106, 123), (106, 124), (106, 125), (106, 126), (106, 127), (106, 128), (106, 129), (106, 130), (106, 131), (106, 134), (106, 135), (106, 136), (106, 137), (106, 138), (106, 139), (106, 140), (106, 141), (106, 142), (106, 144), (106, 146), (106, 147), (106, 148), (106, 149), (106, 151), (106, 152), (106, 153), (106, 154), (106, 157), (106, 158), (106, 159), (106, 160), (106, 161), (106, 162), (106, 164), (106, 194), (108, 42), (108, 61), (108, 76), (108, 109), (108, 110), (108, 114), (109, 42), (109, 91), (109, 113), (109, 164), (110, 76), (111, 114), (112, 114), (114, 0), (114, 26), (114, 29), (114, 30), (114, 31), (114, 35), (114, 36), (114, 40), (114, 42), (114, 44), (114, 47), (114, 49), (114, 53), (114, 55), (114, 56), (114, 57), (114, 59), (114, 61), (114, 64), (114, 74), (114, 75), (114, 81), (114, 82), (114, 86), (114, 91), (114, 93), (114, 96), (114, 107), (114, 99), (114, 100), (114, 101), (114, 102), (114, 109), (114, 129), (114, 134), (114, 135), (114, 140), (114, 164), (114, 179), (115, 10), (115, 31), (115, 164), (116, 114), (119, 150), (120, 157), (121, 137), (122, 137), (123, 163), (124, 117), (124, 125), (124, 130), (124, 150), (124, 163), (125, 126), (126, 117), (126, 135), (127, 134), (128, 135), (129, 36), (129, 91), (130, 131), (131, 134), (131, 135), (132, 157), (133, 137), (134, 36), (134, 74), (134, 109), (134, 135), (135, 36), (135, 74), (135, 136), (135, 156), (136, 36), (137, 134), (138, 139), (139, 135), (140, 107), (140, 134), (140, 136), (141, 118), (141, 135), (141, 144), (142, 36), (142, 61), (142, 64), (142, 83), (142, 118), (142, 129), (142, 134), (142, 135), (142, 136), (142, 140), (142, 141), (142, 143), (142, 144), (142, 150), (142, 152), (142, 156), (142, 158), (142, 162), (142, 164), (142, 195), (143, 135), (144, 36), (144, 134), (144, 135), (144, 136), (144, 162), (145, 134), (146, 134), (146, 135), (146, 155), (147, 29), (147, 44), (147, 46), (147, 47), (147, 118), (147, 134), (147, 135), (147, 136), (147, 140), (147, 144), (147, 156), (147, 158), (147, 164), (148, 136), (148, 150), (149, 134), (149, 135), (149, 136), (149, 141), (150, 134), (150, 164), (151, 150), (152, 134), (152, 135), (152, 156), (152, 162), (153, 134), (153, 135), (153, 162), (154, 150), (155, 134), (156, 135), (157, 134), (158, 136), (158, 140), (159, 135), (160, 134), (160, 135), (160, 155), (162, 36), (162, 61), (162, 74), (162, 96), (162, 134), (162, 135), (162, 144), (167, 171), (168, 83), (169, 99), (170, 83), (170, 85), (171, 2), (172, 195), (173, 78), (174, 78), (175, 60), (175, 66), (175, 70), (175, 142), (176, 94), (176, 120), (176, 121), (176, 122), (176, 123), (176, 132), (176, 133), (176, 137), (176, 138), (176, 145), (176, 157), (177, 12), (177, 26), (177, 27), (177, 28), (177, 29), (177, 30), (177, 31), (177, 33), (177, 34), (177, 35), (177, 36), (177, 44), (177, 55), (177, 56), (177, 57), (177, 58), (177, 59), (177, 61), (177, 62), (177, 63), (177, 64), (177, 74), (177, 75), (177, 78), (177, 79), (177, 81), (177, 82), (177, 86), (177, 89), (177, 90), (177, 91), (177, 93), (177, 94), (177, 96), (177, 107), (177, 99), (177, 100), (177, 101), (177, 102), (177, 109), (177, 113), (177, 118), (177, 128), (177, 129), (177, 134), (177, 135), (177, 136), (177, 139), (177, 140), (177, 141), (177, 144), (177, 148), (177, 149), (177, 150), (177, 151), (177, 152), (177, 153), (177, 154), (177, 159), (177, 162), (178, 35), (180, 37), (182, 31), (183, 31), (184, 185), (185, 29), (185, 30), (185, 31), (185, 44), (185, 79), (185, 166), (185, 187), (185, 190), (187, 185), (188, 164), (188, 187), (188, 190), (189, 108), (190, 185), (192, 193), (195, 164)]

我希望能够更多地展开节点并以分层方式显示它们.

I am hoping to be able to spread out the nodes more and display them in a hierarchical manner.

我希望能够手动移动节点，类似于这个动画，但节点会留在它们所在的位置而不是弹回.但是，如果您可以在不需要手动交互的情况下整齐地显示它们，那也行！

I would prefer to be able to move the nodes around manually , similar to this animation, but with the nodes staying where they are placed instead of snapping back. However, if you can display them neatly without the need for manual interaction, that would work too!

推荐答案

这是一个使用 netgraph 在 networkx 图形对象上.

Here is an MWE using netgraph on a networkx graph object.

import numpy as np
import matplotlib.pyplot as plt; plt.ion()
import networkx
import netgraph # pip install netgraph

# Construct sparse, directed, weighted graph
total_nodes = 20
weights = np.random.rand(total_nodes, total_nodes)
connection_probability = 0.1
is_connected = np.random.rand(total_nodes, total_nodes) <= connection_probability
graph = np.zeros((total_nodes, total_nodes))
graph[is_connected] = weights[is_connected]

# construct a networkx graph
g = networkx.from_numpy_array(graph, networkx.DiGraph)

# decide on a layout
pos = networkx.layout.spring_layout(g)

# Create an interactive plot.
# NOTE: you must retain a reference to the object instance!
# Otherwise the whole thing will be garbage collected after the initial draw
# and you won't be able to move the plot elements around.
plot_instance = netgraph.InteractiveGraph(graph, node_positions=pos)

######## drag nodes around #########

# To access the new node positions:
node_positions = plot_instance.node_positions

这篇关于如何使用鼠标手动放置 networkx 节点?的文章就介绍到这了，希望我们推荐的答案对大家有所帮助，也希望大家多多支持！