"KeyError: Node not in graph" when using pygraphviz_layout even though node is in networkx graph

Question

I have a DataFrame network_df consisting of an edge list

G = nx.from_pandas_edgelist(network_df,source='Parent Node',target= 'Child Node',create_using=nx.DiGraph())

I'm using pygraphviz_layout to calculate the position of each node in G

  pos = pygraphviz_layout(G,prog="dot", args='-Gnodesep=10-Goverlap=false')

But this raises the following error:

Exception has occurred: KeyError
Traceback (most recent call last):
 File "C:\..\Python37\lib\site-packages\pygraphviz\agraph.py", line 1615, in __new__
  nh = gv.agnode(graph.handle, n.encode(graph.encoding), _Action.find)
  KeyError: 'agnode: no key'

  During handling of the above exception, another exception occurred:

  Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "C:\...\Python37\lib\site-packages\networkx\drawing\nx_agraph.py", 
  line 293, in pygraphviz_layout
  node = pygraphviz.Node(A, n)
  File "C:\...\Python37\lib\site- 
  packages\pygraphviz\agraph.py", line 1617, in __new__
    raise KeyError("Node %s not in graph." % n)

  KeyError: "Node ('', '', 'A /// Standard', 'Event A') not in graph."

But when I do

key = ('', '', 'A /// Standard', 'Event A')
print(key in G.nodes())

This prints True meaning that the node is indeed in the Graph, what can I be doing wrong here?

Also, if I use some other function to calculate the position, it works

pos = nx.spring_layout(G)

What is wrong here? pygraphviz_layout has worked without any problems before for other datasets.

Answer 1

The following should work:

import networkx as nx

# an example graph with string (names) as nodes
g = nx.les_miserables_graph()


labels_to_int = {}
int_to_labels = {}
for i, label in enumerate(g):
    labels_to_int[label] = i
    int_to_labels[i] = label

# update labels to ints with
nx.relabel_nodes(g, labels_to_int, copy=False)
print(g.nodes)
# Tested only with the following since I have pygraphviz not installed 
pos = nx.kamada_kawai_layout(g)
# pos = pygraphviz_layout(G,prog="dot", args='-Gnodesep=10-Goverlap=false')

# changes back to original labels
nx.relabel_nodes(g, int_to_labels, copy=False)

label_pos = {label: pos[labels_to_int[label]] for label in g}
print(label_pos)
# {'Napoleon': array([0.73407672, 0.66096404]), 'Myriel': array([0.67744174, 0.53499379]), ....
print(g.nodes)
# ['Napoleon', 'Myriel', ...

Background

The reason for you error is probably that pygraphviz cannot work with arbitrary (hashable) nodes unlike networkx . Therefore, above code simply cast the node labels to int before calling the layout and revert the changes in the nodes and the pos dict.

Answer 2

I've found that using arbitrary hashable nodes doesn't work with the pygraphviz backend, but it does with pydot :

import networkx as nx
from networkx.drawing.nx_pydot import graphviz_layout

g = ...
pos = graphviz_layout(g, "dot")
nx.draw_networkx(g, pos=pos)

The key point here is importing graphviz_layout from networkx.drawing.nx_pydot and not networkx.drawing.nx_agraph or elsewhere.