Python How to pass networkx layout arguments through Bokeh's from_networkx

Question

I'm trying to plot a networkx graph with bokeh using bokeh's from_networkx function with the nx.spring_layout argument. I'm trying to define my graph and its attributes in a pandas dataframe as much as possible. I would like to initialize positions of my nodes; how do I pass these positions to the spring_layout? (If it is passed into the nx.spring_layout(...), I'm not getting the format correct.) Any direction would be helpful.

Put another way, for bokeh.from_networkx(G, networkx.spring_layout...), how to I pass arguments to spring_layout as I would when not using bokeh (e.g., networkx.spring_layout(G, dim=2, k=None, pos=None...))

Simple example:

import networkx as nx
import pandas as pd
from bokeh.models import Plot, ColumnDataSource, Range1d, from_networkx, Circle,MultiLine
from bokeh.io import show, output_file
from bokeh.palettes import Viridis

#define graph
source = ['A', 'A', 'A','a','B','B','B','b']
target = ['a', 'B','b','b','a','b','A','a']
weight = [1,-1000,1,1,1,1, -1000, 1]
df = pd.DataFrame([source,target,weight])
df = df.transpose()
df.columns = ['source','target','weight']
G=nx.from_pandas_dataframe(df, 'source', 'target', ['weight'])

#set node attributes
node_color = {'A':Viridis[10][0], 'B':Viridis[10][9],'a':Viridis[10][4],'b':Viridis[10][4]}
node_size = {'A':50, 'B':40,'a':10,'b':10}
node_initial_pos = {'A':(-0.5,0), 'B':(0.5,0),'a':(0,0.25),'b':(0,-0.25)}
nx.set_node_attributes(G, 'node_color', node_color)
nx.set_node_attributes(G, 'node_size', node_size)
nx.set_node_attributes(G, 'node_initial_pos', node_initial_pos)

#source with node color, size and initial pos (perhaps )
source = ColumnDataSource(pd.DataFrame.from_dict({k:v for k,v in G.nodes(data=True)}, orient='index'))

plot = Plot(plot_width=400, plot_height=400,
            x_range=Range1d(-1.1,1.1), y_range=Range1d(-1.1,1.1))

graph_renderer = from_networkx(G, nx.spring_layout, scale=0.5, center=(0,0))

#style
graph_renderer.node_renderer.data_source = source
graph_renderer.node_renderer.glyph = Circle(fill_color = 'node_color',size = 'node_size', line_color = None)

graph_renderer.edge_renderer.glyph = MultiLine(line_color="#CCCCCC", line_alpha=0.8, line_width=5)


plot.renderers.append(graph_renderer)
output_file('test.html')

show(plot)

Ideally, I wouldn't be creating dictionaries for positions (or color or size), but entering them as part of the df passed to the graph, G.

Bokeh 0.12.14, Networkx 2.1, Python 3.6.3

Answer 1

EDIT: You can pass on the positional argument in the from_networkx(pos=) function.

I tested your code with networkx 2.2 and python 3.5. It works with minor tweaks.

import networkx as nx
import pandas as pd
from bokeh.models import Plot, ColumnDataSource, Range1d, from_networkx, Circle,MultiLine
from bokeh.io import show, output_file
from bokeh.palettes import Viridis

#define graph
source = ['A', 'A', 'A','a','B','B','B','b']
target = ['a', 'B','b','b','a','b','A','a']
weight = [1,-1000,1,1,1,1, -1000, 1]
df = pd.DataFrame([source,target,weight])
df = df.transpose()
df.columns = ['source','target','weight']
G=nx.from_pandas_edgelist(df) # function signature changes

#set node attributes
node_color = {'A':Viridis[10][0], 'B':Viridis[10][9],'a':Viridis[10][4],'b':Viridis[10][4]}
node_size = {'A':50, 'B':40,'a':10,'b':10}
node_initial_pos = {'A':(-0.5,0), 'B':(0.5,0),'a':(0,0.25),'b':(0,-0.25)}
nx.set_node_attributes(G,  node_color, name='node_color') # function signature changes
nx.set_node_attributes(G,  node_size, name='node_size') # function signature changes
nx.set_node_attributes(G,  node_initial_pos, name='node_initial_pos') # function signature changes

#source with node color, size and initial pos (perhaps )
source = ColumnDataSource(pd.DataFrame.from_dict({k:v for k,v in G.nodes(data=True)}, orient='index'))

plot = Plot(plot_width=400, plot_height=400,
            x_range=Range1d(-1.1,1.1), y_range=Range1d(-1.1,1.1))

graph_renderer = from_networkx(G, nx.spring_layout, scale=0.5, center=(0,0), pos=node_initial_pos)

#style
graph_renderer.node_renderer.data_source = source
graph_renderer.node_renderer.glyph = Circle(fill_color = 'node_color',size = 'node_size', line_color = None)

graph_renderer.edge_renderer.glyph = MultiLine(line_color="#CCCCCC", line_alpha=0.8, line_width=5)


plot.renderers.append(graph_renderer)
output_file('test.html')

show(plot)

Output: Without positional argument

Output: With positional argument