python-3.x - 使用 Bokeh : How does one plot variable size nodes, 和节点颜色？

Question

我正在尝试使用 networkx 和 显示图形bokeh 12.7 那

具有基于节点度数的节点大小

基于另一个节点属性的颜色。

期望输出:



数据设置

import pandas as pd
import numpy as np
import networkx as nx
import seaborn as sns

from bokeh.io import show, output_notebook  #output_file,
from bokeh.plotting import figure
from bokeh.models.graphs import from_networkx

from bokeh.models import GraphRenderer, StaticLayoutProvider, LinearColorMapper, ColumnDataSource
from bokeh.palettes import Spectral8, Spectral4

G = nx.karate_club_graph()

# Some Random index
node_color = {k:v for k, v  in enumerate(np.random.uniform(low=0, high=21, size=(G.number_of_nodes(),)).round(1))}

# Set node attributes
nx.set_node_attributes(G, 'node_color', node_color)
nx.set_node_attributes(G, 'node_size', G.degree())

尝试使用 bokeh 绘图与 cubehelix_palette

# Map cubehelix_palette
palette = sns.cubehelix_palette(21)
pal_hex_lst = palette.as_hex()

mapper = LinearColorMapper(palette=pal_hex_lst, low=0, high=21)

# Initiate bokeh plot
plot = figure(title="Resized Node Demo", x_range=(-1.1,1.1), y_range=(-1.1,1.1),
              tools="", toolbar_location=None)

# Graph renderer using nx
graph = from_networkx(G, nx.spring_layout, scale=2, center=(0,0))

# Style node
graph.node_renderer.glyph = Circle(size='node_size', fill_color={'field': 'node_color', 'transform': mapper})


plot.renderers.append(graph)

output_notebook()
#output_file("networkx_graph.html")
show(plot)

这给出了这个错误: Glyph refers to nonexistent column name


我也试过这个:

# 1. Create Plot container
plot = figure(title=endNode, x_range=(-1.1,1.1), y_range=(-1.1,1.1),
              tools="", toolbar_location=None)

# 2. Create graph plot comtainer
graph = GraphRenderer()

node_link_dict = nx.readwrite.json_graph.node_link_data(G)
node_df = pd.DataFrame(node_link_dict['nodes'])

node_cds = ColumnDataSource.from_df(graph_data.node_df)
graph.node_renderer.data_source.data = node_cds


# 3. Set Node Style
graph.node_renderer.glyph = Circle(size='node_size', fill_color='node_color')

有什么想法吗？

Answer 1

我也试图根据度中心性设置节点大小，并且能够使用

graph.node_renderer.data_source = source

我可以看到不同的尺寸和颜色(见附图)，虽然我还没有找到以下错误的原因

E-1010 (CDSVIEW_SOURCE_DOESNT_MATCH): CDSView used by Glyph renderer must have a source that matches the Glyph renderer's data source: GlyphRenderer(id='035dd78a-7bff-40d1-8357-d7193222ca02', ...)

    #just to make the sizes visible
    node_size = {k:5*v for k,v in G.degree().items()} 


### set node attributes
    nx.set_node_attributes(G, 'node_color', node_color)
    nx.set_node_attributes(G, 'node_size', node_size)

    source=ColumnDataSource(pd.DataFrame.from_dict({k:v for k,v in G.nodes(data=True)},orient='index'))
    mapper = LinearColorMapper(palette=pal_hex_lst, low=0, high=21)

### Initiate bokeh plot
    plot = figure(title="Resized Node Demo", x_range=(-1.1,1.1), y_range=(-1.1,1.1),
              tools="", toolbar_location=None)

    # Graph renderer using nx
    graph = from_networkx(G, nx.spring_layout, scale=2, center=(0,0))

    # Style node
    graph.node_renderer.data_source = source
    graph.node_renderer.glyph = Circle(size='node_size', fill_color={'field': 'node_color', 'transform': mapper})


    plot.renderers.append(graph)