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I am trying to draw network graphs following from this example.

Below is what I am trying to do.

`data = {
    'source': ['A', 'C', 'B', 'F', 'G'],
    'target': ['B', 'D', 'E', 'C', 'E'],
    'weight': [5, 3, 10, 4, 7]
}
df = pd.DataFrame(data=data)
G = networkx.from_pandas_edgelist(df, 'source', 'target', 'weight')
# Choose a title!
title = 'Graph Network'

# Establish which categories will appear when hovering over each node
HOVER_TOOLTIPS = [("Character", "@index")]
# Create a plot — set dimensions, toolbar, and title
plot = figure(tooltips=HOVER_TOOLTIPS,
              tools="pan,wheel_zoom,save,reset", active_scroll='wheel_zoom',
              x_range=Range1d(-10.1, 10.1), y_range=Range1d(-10.1, 10.1), title=title)

network_graph = from_networkx(G, networkx.spring_layout, scale=10, center=(0, 0))

# Set node size and color
network_graph.node_renderer.glyph = Circle(size=15, fill_color='skyblue')

# Set edge opacity and width
network_graph.edge_renderer.glyph = MultiLine(line_alpha=0.5, line_width=1)

# Add network graph to the plot
plot.renderers.append(network_graph)

return plot`

The error I get is as below;

failed to validate StaticLayoutProvider(id='p1075', ...).graph_layout: expected an 
element of Dict(Int, Seq(Any)), got {'A': array([-7.94707039,  3.45521447]), 'B': 
array([-6.60505319,  4.31869148]), 'C': array([ 8.38746457, -6.26423001]), 'D': 
array([ 6.7178286 , -6.63523276]), 'E': array([-5.66671517,  5.25260372]), 'F': 
array([10.        , -6.53836091]), 'G': array([-4.88645443,  6.41131401])}

The error is self-explanatory. The engine expects an integer as a key, but I pass a String into it.

This error is similar to this stack overflow question

However in this case, the error specifies expected an element of Dict(Either(String, Int), Seq(Any)) that both String and Int are allowed. While in my case, the error specifies that only ints are allowed.

And indeed if I simulate the source and target as integers, the graph is drawn successfully.

If it helps, I am using networkx~=2.8.8 and bokeh==3.0.3.

Can anyone help me identify what I am doing wrong.

unlockme
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    This looks like a regression. I was running your example with bokeh 2.4.3 without problems. Maybe it is worth to open an [issue](https://github.com/bokeh/bokeh/issues) on GitHub. As long as only integers are supported, you can run `df.source=df.source.apply(ord)` etc. – mosc9575 Dec 25 '22 at 23:11
  • FYI, bokeh has a nice example for [networkx](https://docs.bokeh.org/en/latest/docs/examples/topics/graph/from_networkx.html). – mosc9575 Dec 25 '22 at 23:13
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    Thanks @mosc9575, changing bokeh to 2.4.3 does not raise the error. – unlockme Dec 28 '22 at 19:43

2 Answers2

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I have the same problem using BokehJS 3.2.1. My nodes are strings attached using add_edge and

graph = from_networkx(nxg, nx.spring_layout)

fails with

ValueError: failed to validate StaticLayoutProvider(id='p1141', ...).graph_layout: expected an element of Dict(Int, Seq(Any)), got ...
Andrew Spruce
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  • Hi @Andrew Spruce this is more of a comment/question than an answer. Please follow guidelines. – unlockme Aug 10 '23 at 07:07
  • Your answer could be improved with additional supporting information. Please [edit] to add further details, such as citations or documentation, so that others can confirm that your answer is correct. You can find more information on how to write good answers [in the help center](/help/how-to-answer). – Community Aug 10 '23 at 15:01
  • This does not really answer the question. If you have a different question, you can ask it by clicking [Ask Question](https://stackoverflow.com/questions/ask). To get notified when this question gets new answers, you can [follow this question](https://meta.stackexchange.com/q/345661). Once you have enough [reputation](https://stackoverflow.com/help/whats-reputation), you can also [add a bounty](https://stackoverflow.com/help/privileges/set-bounties) to draw more attention to this question. - [From Review](/review/late-answers/34802585) – d1sh4 Aug 12 '23 at 14:33
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I think it is still an open bug in https://github.com/bokeh/bokeh/issues/12651

My solution is to create new Graph H, and relabel it with integer.

mapping = dict((n, i) for i, n in enumerate(G.nodes))
H = networkx.relabel_nodes(G, mapping)

Then draw from the graph H.

Khoiri Uswanto
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