def render_graph(graph, add_parent=False, default_color='white'):
g_copy = graph.copy()
_scale_edges(g_copy)
if add_parent:
g_copy = _add_parent_term(g_copy)
_set_node_color(g_copy, default_color)
d = nx_to_json(g_copy)
u_name = "cy{}".format(uuid.uuid4())
d['uuid'] = u_name
d['style_json'] = json.dumps(styles['default'])
edge_types = set()
for i, j, data in graph.edges(data=True):
if 'interactionType' in data:
for e in data['interactionType'].split('|'):
edge_types.add(e)
d['edge_list'] = list(edge_types)
fname_temp = '{}.html'.format(u_name)
subgraph_html = env.get_template('subgraph.html')
template = env.get_template('main_view.html')
with open(fname_temp, 'w') as f:
f.write(subgraph_html.render(d))
display(HTML(template.render(name=u_name, filename=fname_temp)))
def draw_cyjs(graph, add_parent=False, layout='cose-bilkent',
bg_color='white', default_node_color='white', **layout_args):
""" Renders a graph using cytoscape.js
Parameters
----------
graph : nx.DiGraph
add_parent : bool
Group together nodes that share 'termName'.
layout : str
Layout
bg_color
default_node_color : str
Will only be used if color is not already set for node
layout_args : dict
Any additional arguments for use in cytoscape.js. Examples can be found
in cyjs_options.py
Returns
-------
"""
# Dont think users need these
height = 700
width = 100
g_copy = graph.copy()
if add_parent:
g_copy = _add_parent_term(g_copy)
_scale_edges(g_copy)
_set_node_color(g_copy, default_node_color)
d = nx_to_json(g_copy)
d['background'] = bg_color
d['uuid'] = "cy" + str(uuid.uuid4())
d['widget_width'] = str(width)
d['widget_height'] = str(height)
if layout not in layouts:
raise Exception(
"layout {} is not in {}".format(layout, layouts.keys())
)
else:
layout_opts = layouts[layout].copy()
layout_opts.update(layout_args)
d['layout_json'] = json.dumps(layout_opts)
d['style_json'] = json.dumps(styles['default'])
d['fitbutton'] = "fit{}".format(uuid.uuid4())
template = env.get_template('subgraph_2.html')
display(HTML(template.render(d)))
def test_nx_to_json():
g = nx.DiGraph()
g.add_edge('a', 'b')
json_g = exporters.nx_to_json(g)
answer = {'edges': '[{"data": {"source": "a", "target": "b"}}]',
'nodes': '[{"data": {"id": "a", "name": "a"}},'
' {"data": {"id": "b", "name": "b"}}]'}
a_edges = json.loads(json_g['edges'])
b_edges = json.loads(answer['edges'])
a_nodes = json.loads(json_g['nodes'])
b_nodes = json.loads(answer['nodes'])
ok_(ordered(a_edges) == ordered(b_edges))
ok_(ordered(a_nodes) == ordered(b_nodes))
def test_nx_to_json():
g = nx.DiGraph()
g.add_edge('a', 'b')
json_g = exporters.nx_to_json(g)
answer = {
'edges':
'[{"data": {"source": "a", "target": "b"}}]',
'nodes':
'[{"data": {"id": "a", "name": "a"}},'
' {"data": {"id": "b", "name": "b"}}]'
}
a_edges = json.loads(json_g['edges'])
b_edges = json.loads(answer['edges'])
a_nodes = json.loads(json_g['nodes'])
b_nodes = json.loads(answer['nodes'])
assert ordered(a_edges) == ordered(b_edges)
assert ordered(a_nodes) == ordered(b_nodes)
def display_graph(graph,
add_parent=False,
layout_algorithm='cose-bilkent',
background='#FFFFFF',
height=700,
width=100):
g_copy = graph.copy()
if add_parent:
g_copy = _add_parent_term(g_copy)
d = nx_to_json(g_copy)
d['background'] = background
d['uuid'] = "cy" + str(uuid.uuid4())
d['widget_width'] = str(width)
d['widget_height'] = str(height)
d['layout'] = layout_algorithm
d['style_json'] = json.dumps(styles['default'])
d['fitbutton'] = "fit" + str(uuid.uuid4())
template = env.get_template('subgraph_2.html')
widget = template.render(d)
display(HTML(widget))
def prep_g(sg):
data = nx_to_json(sg)
data['edge_list'] = _get_edge_types(sg)
data['style_json'] = styles['default']
return data