python - 当networkx中有数百个节点时，如何避免重叠？

Question

我有2000多个节点和900多个边，但是当我尝试在networkx中制作图形时，我发现所有节点都挤在一起。我尝试更改属性值，例如小数位数，k。我发现它们没有用，因为下面有数百个带有标签的节点，这意味着我无法选择小尺寸的节点。我想知道是否有一种方法可以扩展 Canvas 或使用其他方法来增加节点的距离以避免重叠，因此我可以清楚地看到每个节点及其标签。
谢谢

Answer 1

您可以通过 ploty 使用交互式图形来绘制大量节点和边线。您可以更改每个属性，例如 Canvas 大小等，并通过缩放其他操作更轻松地将其可视化。
例子:
导入绘图

import plotly.graph_objects as go

import networkx as nx

在一条轨迹中将边线添加为不连续的线，并在散点线中添加节点

G = nx.random_geometric_graph(200, 0.125)
edge_x = []
edge_y = []
for edge in G.edges():
    x0, y0 = G.nodes[edge[0]]['pos']
    x1, y1 = G.nodes[edge[1]]['pos']
    edge_x.append(x0)
    edge_x.append(x1)
    edge_x.append(None)
    edge_y.append(y0)
    edge_y.append(y1)
    edge_y.append(None)

edge_trace = go.Scatter(
    x=edge_x, y=edge_y,
    line=dict(width=0.5, color='#888'),
    hoverinfo='none',
    mode='lines')

node_x = []
node_y = []
for node in G.nodes():
    x, y = G.nodes[node]['pos']
    node_x.append(x)
    node_y.append(y)

node_trace = go.Scatter(
    x=node_x, y=node_y,
    mode='markers',
    hoverinfo='text',
    marker=dict(
        showscale=True,
        # colorscale options
        #'Greys' | 'YlGnBu' | 'Greens' | 'YlOrRd' | 'Bluered' | 'RdBu' |
        #'Reds' | 'Blues' | 'Picnic' | 'Rainbow' | 'Portland' | 'Jet' |
        #'Hot' | 'Blackbody' | 'Earth' | 'Electric' | 'Viridis' |
        colorscale='YlGnBu',
        reversescale=True,
        color=[],
        size=10,
        colorbar=dict(
            thickness=15,
            title='Node Connections',
            xanchor='left',
            titleside='right'
        ),
        line_width=2))

通过连接数为节点指定颜色。
另一种选择是通过连接数来调整点的大小，即node_trace.marker.size = node_adjacencies

node_adjacencies = []
node_text = []
for node, adjacencies in enumerate(G.adjacency()):
    node_adjacencies.append(len(adjacencies[1]))
    node_text.append('# of connections: '+str(len(adjacencies[1])))

node_trace.marker.color = node_adjacencies
node_trace.text = node_text

创建网络图

fig = go.Figure(data=[edge_trace, node_trace],
             layout=go.Layout(
                title='<br>Network graph made with Python',
                titlefont_size=16,
                showlegend=False,
                hovermode='closest',
                margin=dict(b=20,l=5,r=5,t=40),
                annotations=[ dict(
                    text="Python code: <a href='https://plotly.com/ipython-notebooks/network-graphs/'> https://plotly.com/ipython-notebooks/network-graphs/</a>",
                    showarrow=False,
                    xref="paper", yref="paper",
                    x=0.005, y=-0.002 ) ],
                xaxis=dict(showgrid=False, zeroline=False, showticklabels=False),
                yaxis=dict(showgrid=False, zeroline=False, showticklabels=False))
                )
fig.show()

您可以在Internet上获得有关ploty的更多详细信息
查看文档: https://plotly.com/python/network-graphs/