File size: 5,841 Bytes
1e321d6 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 | import networkx as nx
__all__ = ["cytoscape_data", "cytoscape_graph"]
def cytoscape_data(G, name="name", ident="id"):
"""Returns data in Cytoscape JSON format (cyjs).
Parameters
----------
G : NetworkX Graph
The graph to convert to cytoscape format
name : string
A string which is mapped to the 'name' node element in cyjs format.
Must not have the same value as `ident`.
ident : string
A string which is mapped to the 'id' node element in cyjs format.
Must not have the same value as `name`.
Returns
-------
data: dict
A dictionary with cyjs formatted data.
Raises
------
NetworkXError
If the values for `name` and `ident` are identical.
See Also
--------
cytoscape_graph: convert a dictionary in cyjs format to a graph
References
----------
.. [1] Cytoscape user's manual:
http://manual.cytoscape.org/en/stable/index.html
Examples
--------
>>> from pprint import pprint
>>> G = nx.path_graph(2)
>>> cyto_data = nx.cytoscape_data(G)
>>> pprint(cyto_data, sort_dicts=False)
{'data': [],
'directed': False,
'multigraph': False,
'elements': {'nodes': [{'data': {'id': '0', 'value': 0, 'name': '0'}},
{'data': {'id': '1', 'value': 1, 'name': '1'}}],
'edges': [{'data': {'source': 0, 'target': 1}}]}}
The :mod:`json` package can be used to serialize the resulting data
>>> import io, json
>>> with io.StringIO() as fh: # replace io with `open(...)` to write to disk
... json.dump(cyto_data, fh)
... fh.seek(0) # doctest: +SKIP
... print(fh.getvalue()[:64]) # View the first 64 characters
{"data": [], "directed": false, "multigraph": false, "elements":
"""
if name == ident:
raise nx.NetworkXError("name and ident must be different.")
jsondata = {"data": list(G.graph.items())}
jsondata["directed"] = G.is_directed()
jsondata["multigraph"] = G.is_multigraph()
jsondata["elements"] = {"nodes": [], "edges": []}
nodes = jsondata["elements"]["nodes"]
edges = jsondata["elements"]["edges"]
for i, j in G.nodes.items():
n = {"data": j.copy()}
n["data"]["id"] = j.get(ident) or str(i)
n["data"]["value"] = i
n["data"]["name"] = j.get(name) or str(i)
nodes.append(n)
if G.is_multigraph():
for e in G.edges(keys=True):
n = {"data": G.adj[e[0]][e[1]][e[2]].copy()}
n["data"]["source"] = e[0]
n["data"]["target"] = e[1]
n["data"]["key"] = e[2]
edges.append(n)
else:
for e in G.edges():
n = {"data": G.adj[e[0]][e[1]].copy()}
n["data"]["source"] = e[0]
n["data"]["target"] = e[1]
edges.append(n)
return jsondata
@nx._dispatchable(graphs=None, returns_graph=True)
def cytoscape_graph(data, name="name", ident="id"):
"""
Create a NetworkX graph from a dictionary in cytoscape JSON format.
Parameters
----------
data : dict
A dictionary of data conforming to cytoscape JSON format.
name : string
A string which is mapped to the 'name' node element in cyjs format.
Must not have the same value as `ident`.
ident : string
A string which is mapped to the 'id' node element in cyjs format.
Must not have the same value as `name`.
Returns
-------
graph : a NetworkX graph instance
The `graph` can be an instance of `Graph`, `DiGraph`, `MultiGraph`, or
`MultiDiGraph` depending on the input data.
Raises
------
NetworkXError
If the `name` and `ident` attributes are identical.
See Also
--------
cytoscape_data: convert a NetworkX graph to a dict in cyjs format
References
----------
.. [1] Cytoscape user's manual:
http://manual.cytoscape.org/en/stable/index.html
Examples
--------
>>> data_dict = {
... "data": [],
... "directed": False,
... "multigraph": False,
... "elements": {
... "nodes": [
... {"data": {"id": "0", "value": 0, "name": "0"}},
... {"data": {"id": "1", "value": 1, "name": "1"}},
... ],
... "edges": [{"data": {"source": 0, "target": 1}}],
... },
... }
>>> G = nx.cytoscape_graph(data_dict)
>>> G.name
''
>>> G.nodes()
NodeView((0, 1))
>>> G.nodes(data=True)[0]
{'id': '0', 'value': 0, 'name': '0'}
>>> G.edges(data=True)
EdgeDataView([(0, 1, {'source': 0, 'target': 1})])
"""
if name == ident:
raise nx.NetworkXError("name and ident must be different.")
multigraph = data.get("multigraph")
directed = data.get("directed")
if multigraph:
graph = nx.MultiGraph()
else:
graph = nx.Graph()
if directed:
graph = graph.to_directed()
graph.graph = dict(data.get("data"))
for d in data["elements"]["nodes"]:
node_data = d["data"].copy()
node = d["data"]["value"]
if d["data"].get(name):
node_data[name] = d["data"].get(name)
if d["data"].get(ident):
node_data[ident] = d["data"].get(ident)
graph.add_node(node)
graph.nodes[node].update(node_data)
for d in data["elements"]["edges"]:
edge_data = d["data"].copy()
sour = d["data"]["source"]
targ = d["data"]["target"]
if multigraph:
key = d["data"].get("key", 0)
graph.add_edge(sour, targ, key=key)
graph.edges[sour, targ, key].update(edge_data)
else:
graph.add_edge(sour, targ)
graph.edges[sour, targ].update(edge_data)
return graph
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