python - 将 networkx 2D 图转换为 3D 交互式图

Question

我在 networkx 中有以下图表:

import matplotlib.pyplot as plt
import networkx as nx

G = nx.Graph()
G.add_edge(1, 2, weight = 1)
G.add_edge(2, 3, weight = 3)
G.add_edge(4, 5, weight = 2)
G.add_edge(6, 3, weight = 4)
G.add_edge(6, 4, weight = 6)


plt.figure(figsize=(12,12))
edges = G.edges()
pos = nx.spring_layout(G, k = 0.5) # k regulates the distance between nodes
weights = [G[u][v]['weight'] for u,v in edges]
nx.draw(G, with_labels=True, node_color='skyblue', font_weight='bold',  width=weights, pos=pos)

有没有办法将这个 2D 图形转换为 3D 图形？坐标无所谓。我只对绘图的交互能力感兴趣(即我能够旋转图形)。我知道 plotly有能力做这样的 plots ，但我不确定如何组合我的 2D networkx图和 plotly以这种方式

Answer 1

免责声明:我无论如何都不是 networkx 的专家，所以 this article在回答您的问题时非常有值(value)。我已经适应了代码以尽可能适合您的示例。
我们首先要设置参数dim=3打电话时nx.spring_layout以确保您的坐标为 3D。然后我们提取所有节点和边的 x、y、z 坐标，并通过跟踪将它们传递到 go.Scatter3d Plotly 中的方法。
更新:要在悬停文本中添加权重，我们可以将它们 anchor 定到边缘之间的中点，如 here 所述。 .

# import matplotlib.pyplot as plt
import plotly.graph_objects as go
import networkx as nx

G = nx.Graph()
G.add_edge(1, 2, weight = 1)
G.add_edge(2, 3, weight = 3)
G.add_edge(4, 5, weight = 2)
G.add_edge(6, 3, weight = 4)
G.add_edge(6, 4, weight = 6)

edge_weights =[1,3,2,4,6]

Num_nodes = len(G.nodes)

# plt.figure(figsize=(5,5))
edges = G.edges()

# ## update to 3d dimension
spring_3D = nx.spring_layout(G, dim = 3, k = 0.5) # k regulates the distance between nodes
# weights = [G[u][v]['weight'] for u,v in edges]
# nx.draw(G, with_labels=True, node_color='skyblue', font_weight='bold',  width=weights, pos=pos)

# we need to seperate the X,Y,Z coordinates for Plotly
# NOTE: spring_3D is a dictionary where the keys are 1,...,6
x_nodes= [spring_3D[key][0] for key in spring_3D.keys()] # x-coordinates of nodes
y_nodes = [spring_3D[key][1] for key in spring_3D.keys()] # y-coordinates
z_nodes = [spring_3D[key][2] for key in spring_3D.keys()] # z-coordinates

#we need to create lists that contain the starting and ending coordinates of each edge.
x_edges=[]
y_edges=[]
z_edges=[]

#create lists holding midpoints that we will use to anchor text
xtp = []
ytp = []
ztp = []

#need to fill these with all of the coordinates
for edge in edges:
    #format: [beginning,ending,None]
    x_coords = [spring_3D[edge[0]][0],spring_3D[edge[1]][0],None]
    x_edges += x_coords
    xtp.append(0.5*(spring_3D[edge[0]][0]+ spring_3D[edge[1]][0]))

    y_coords = [spring_3D[edge[0]][1],spring_3D[edge[1]][1],None]
    y_edges += y_coords
    ytp.append(0.5*(spring_3D[edge[0]][1]+ spring_3D[edge[1]][1]))

    z_coords = [spring_3D[edge[0]][2],spring_3D[edge[1]][2],None]
    z_edges += z_coords
    ztp.append(0.5*(spring_3D[edge[0]][2]+ spring_3D[edge[1]][2])) 


etext = [f'weight={w}' for w in edge_weights]

trace_weights = go.Scatter3d(x=xtp, y=ytp, z=ztp,
    mode='markers',
    marker =dict(color='rgb(125,125,125)', size=1), #set the same color as for the edge lines
    text = etext, hoverinfo='text')

#create a trace for the edges
trace_edges = go.Scatter3d(
    x=x_edges,
    y=y_edges,
    z=z_edges,
    mode='lines',
    line=dict(color='black', width=2),
    hoverinfo='none')

#create a trace for the nodes
trace_nodes = go.Scatter3d(
    x=x_nodes,
    y=y_nodes,
    z=z_nodes,
    mode='markers',
    marker=dict(symbol='circle',
            size=10,
            color='skyblue')
    )

#Include the traces we want to plot and create a figure
data = [trace_edges, trace_nodes, trace_weights]
fig = go.Figure(data=data)

fig.show()