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Bookeh failed to validate StaticLayoutProvider(id='5785', ...).graph_layout

I am in a very wired situation. So, I am trying to visualize a graph using Bokeh. The graph has nodes as nodes IDs, which are connected by sticks that have length and also IDs. For example, I have the following DataFrame of sticks:

import pandas as pd
import networkx as nx

d = {'Node 1': [56416, 56416], 'Node 2': [76449, 76448], 'len': [45, 146], 'Stick ID': [25788, 25789]}
df = pd.DataFrame(data=d)

which looks like:

df
Out[82]: 
   Node 1  Node 2  len  Stick ID
0   56416   76449   45     25788
1   56416   76448  146     25789

Next, I'm buliding a graph which I want to visualize using Bokeh.

G_1=nx.from_pandas_edgelist(df, 'Node 1', 'Node 2', ['Stick ID', 'len']) # Length and Stick ID are wights for the edges

from bokeh.io import output_file, show
from bokeh.plotting import figure, from_networkx

plot = figure(title="Networkx Integration Demonstration", x_range=(-10.1,10.1), y_range=(-10.1,10.1),
              tools="", toolbar_location=None)

graph = from_networkx(G_1, nx.spring_layout, scale=2, center=(0,0))
plot.renderers.append(graph)

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

And it works, I'm getting the following picture enter image description here

However! When I try to visualize a DataFrame with all my data, I'm getting the following error when calling from_network:

ValueError: failed to validate StaticLayoutProvider(id='5319', ...).graph_layout: expected an element of Dict(Either(String, Int), Seq(Any)), got {55331.0: array([0.63049136, 0.20157234]), 76996.0: array([0.74836386, 0.17916439]),..... and so on the whole dictionary of my data

The DataFrame with the data has the exactly identical structure!

df.head()
Out[88]: 
    Node 1   Node 2        len  Stick ID
0  55331.0  76996.0  15.269983   25594.0
1  55844.0  60447.0   4.457858   25595.0
2  55624.0  76989.0  21.560522   25736.0
3  54578.0  76990.0  28.195875   25737.0
4  56416.0  76491.0  54.661070   25788.0

When I'm just plotting my Data with matplotlib. I have no problem:

pos = graphviz_layout(G_1, prog='neato')
fig, ax = plt.subplots()
nx.draw_networkx(G_1, pos=pos)
fig.tight_layout()
fig.show()

enter image description here

Can someone help to figure out what wrong I'm doing with Bokeh?

There was a similar question before, but there is no solution posted.

Network graph error: failed to validate StaticLayoutProvider(id='1058', ...).graph_layout:

Solution

  • It's a speculation only since there is no reproducible code, but one potential source of the error is the float node IDs. This could happen because of a missing value somewhere in the data frame. A quick fix would be to run:

    df = df.dropna().astype({'Node 1': 'int', 'Node 2': 'int'})
# the rest of your code, starting with `nx.from_pandas_edgelist` line

    Note that for confidence in results one would want to investigate where the missing values originated from and make appropriate adjustments.