Source code for bokeh.plotting.graph
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# Copyright (c) 2012 - 2024, Anaconda, Inc., and Bokeh Contributors.
# All rights reserved.
#
# The full license is in the file LICENSE.txt, distributed with this software.
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# Boilerplate
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from __future__ import annotations
import logging # isort:skip
log = logging.getLogger(__name__)
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# Imports
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# Bokeh imports
from ..models.graphs import StaticLayoutProvider
from ..models.renderers import GraphRenderer
from ..util.warnings import warn
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# Globals and constants
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__all__ = (
'from_networkx'
)
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# General API
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[docs]
def from_networkx(graph, layout_function, **kwargs):
'''
Generate a ``GraphRenderer`` from a ``networkx.Graph`` object and networkx
layout function. Any keyword arguments will be passed to the
layout function.
Only two dimensional layouts are supported.
Args:
graph (networkx.Graph) : a networkx graph to render
layout_function (function or dict) : a networkx layout function or mapping of node keys to positions.
The position is a two element sequence containing the x and y coordinate.
Returns:
instance (GraphRenderer)
.. note::
Node and edge attributes may be lists or tuples. However, a given
attribute must either have *all* lists or tuple values, or *all*
scalar values, for nodes or edges it is defined on.
.. warning::
Node attributes labeled 'index' and edge attributes labeled 'start' or 'end' are ignored.
If you want to convert these attributes, please re-label them to other names.
Raises:
ValueError
'''
# Handles nx 1.x vs 2.x data structure change
# Convert node attributes
node_dict = dict()
node_attr_keys = [attr_key for node in list(graph.nodes(data=True))
for attr_key in node[1].keys()]
node_attr_keys = list(set(node_attr_keys))
for attr_key in node_attr_keys:
values = [node_attr[attr_key] if attr_key in node_attr.keys() else None
for _, node_attr in graph.nodes(data=True)]
values = _handle_sublists(values)
node_dict[attr_key] = values
if 'index' in node_attr_keys:
warn("Converting node attributes labeled 'index' are skipped. "
"If you want to convert these attributes, please re-label with other names.")
node_dict['index'] = list(graph.nodes())
# Convert edge attributes
edge_dict = dict()
edge_attr_keys = [attr_key for edge in graph.edges(data=True)
for attr_key in edge[2].keys()]
edge_attr_keys = list(set(edge_attr_keys))
for attr_key in edge_attr_keys:
values = [edge_attr[attr_key] if attr_key in edge_attr.keys() else None
for _, _, edge_attr in graph.edges(data=True)]
values = _handle_sublists(values)
edge_dict[attr_key] = values
if 'start' in edge_attr_keys or 'end' in edge_attr_keys:
warn("Converting edge attributes labeled 'start' or 'end' are skipped. "
"If you want to convert these attributes, please re-label them with other names.")
edge_dict['start'] = [x[0] for x in graph.edges()]
edge_dict['end'] = [x[1] for x in graph.edges()]
graph_renderer = GraphRenderer()
graph_renderer.node_renderer.data_source.data = node_dict
graph_renderer.edge_renderer.data_source.data = edge_dict
if callable(layout_function):
graph_layout = layout_function(graph, **kwargs)
else:
graph_layout = layout_function
node_keys = graph_renderer.node_renderer.data_source.data['index']
if set(node_keys) != set(layout_function.keys()):
warn("Node keys in 'layout_function' don't match node keys in the graph. "
"These nodes may not be displayed correctly.")
graph_renderer.layout_provider = StaticLayoutProvider(graph_layout=graph_layout)
return graph_renderer
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# Dev API
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# Private API
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def _handle_sublists(values):
# if any of the items is non-scalar, they all must be
if any(isinstance(x, (list, tuple)) for x in values):
if not all(isinstance(x, (list, tuple)) for x in values if x is not None):
raise ValueError("Can't mix scalar and non-scalar values for graph attributes")
return [[] if x is None else list(x) for x in values]
return values
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# Code
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