From 0cd86c11a40086548dfc438977c674bb2eebca0e Mon Sep 17 00:00:00 2001
From: Hui Lan <lanhui@zjnu.edu.cn>
Date: Fri, 14 Aug 2020 23:24:00 +0800
Subject: html_network.py: make URL for edge information such as
 AT3G09600_AT1G49720_0.html correct.

---
 Code/util_networkx.py | 151 ++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 151 insertions(+)
 create mode 100755 Code/util_networkx.py

(limited to 'Code/util_networkx.py')

diff --git a/Code/util_networkx.py b/Code/util_networkx.py
new file mode 100755
index 0000000..b708610
--- /dev/null
+++ b/Code/util_networkx.py
@@ -0,0 +1,151 @@
+"""
+Data conversion utility for NetworkX
+=====================================
+
+Convert cytoscape.js style graphs from/to NetworkX object.
+
+https://networkx.github.io/
+
+"""
+
+import networkx as nx
+
+# Special Keys
+ID = 'id'
+NAME = 'name'
+DATA = 'data'
+ELEMENTS = 'elements'
+
+NODES = 'nodes'
+EDGES = 'edges'
+
+SOURCE = 'source'
+TARGET = 'target'
+
+DEF_SCALE = 100
+
+
+def __map_table_data(columns, graph_obj):
+    data = {}
+    for col in columns:
+        if col == 0:
+            break
+
+        data[col] = graph_obj[col]
+
+    return data
+
+
+def __create_node(node, node_id):
+    new_node = {}
+    node_columns = node.keys()
+    data = __map_table_data(node_columns, node)
+    # Override special keys
+    data[ID] = str(node_id)
+    data[NAME] = str(node_id)
+
+    if 'position' in node.keys():
+        position = node['position']
+        new_node['position'] = position
+
+    new_node[DATA] = data
+    return new_node
+
+
+def __build_multi_edge(edge_tuple, g):
+    source = edge_tuple[0]
+    target = edge_tuple[1]
+    key = edge_tuple[2]
+    data = edge_tuple[3]
+
+    data['source'] = str(source)
+    data['target'] = str(target)
+    data['interaction'] = str(key)
+    return {DATA: data}
+
+
+def __build_edge(edge_tuple, g):
+    source = edge_tuple[0]
+    target = edge_tuple[1]
+    data = edge_tuple[2]
+
+    data['source'] = str(source)
+    data['target'] = str(target)
+    return {DATA: data}
+
+
+def __build_empty_graph():
+    return {
+        DATA: {},
+        ELEMENTS: {
+            NODES: [],
+            EDGES: []
+        }
+    }
+
+
+def from_networkx(g, layout=None, scale=DEF_SCALE):
+    # Dictionary Object to be converted to Cytoscape.js JSON
+    cygraph = __build_empty_graph()
+
+    if layout is not None:
+        pos = map(lambda position:
+                  {'x': position[0]*scale, 'y': position[1]*scale},
+                  layout.values())
+
+    nodes = g.nodes()
+    if isinstance(g, nx.MultiDiGraph) or isinstance(g, nx.MultiGraph):
+        edges = g.edges(data=True, keys=True)
+        edge_builder = __build_multi_edge
+    else:
+        edges = g.edges(data=True)
+        edge_builder = __build_edge
+
+    # Map network table data
+    cygraph[DATA] = __map_table_data(g.graph.keys(), g.graph)
+
+    for i, node_id in enumerate(nodes):
+        new_node = __create_node(g.node[node_id], node_id)
+        if layout is not None:
+            new_node['position'] = pos[i]
+
+        cygraph['elements']['nodes'].append(new_node)
+
+    for edge in edges:
+        cygraph['elements']['edges'].append(edge_builder(edge, g))
+
+    return cygraph['elements']
+
+
+def to_networkx(cyjs, directed=True):
+    """
+    Convert Cytoscape.js-style JSON object into NetworkX object.
+
+    By default, data will be handles as a directed graph.
+    """
+
+    if directed:
+        g = nx.MultiDiGraph()
+    else:
+        g = nx.MultiGraph()
+
+    network_data = cyjs[DATA]
+    if network_data is not None:
+        for key in network_data.keys():
+            g.graph[key] = network_data[key]
+
+    nodes = cyjs[ELEMENTS][NODES]
+    edges = cyjs[ELEMENTS][EDGES]
+
+    for node in nodes:
+        data = node[DATA]
+        g.add_node(data[ID], attr_dict=data)
+
+    for edge in edges:
+        data = edge[DATA]
+        source = data[SOURCE]
+        target = data[TARGET]
+
+        g.add_edge(source, target, attr_dict=data)
+
+    return g
-- 
cgit v1.2.1