Merge branch 'master' of github.com:benmaier/netwulf

netwulf/interactive.py

@@ -171,15 +171,16 @@ def log_message(self, format, *args):
 def visualize(network,
               port=9853,
               verbose=False,
-              config=None):
+              config=None,
+              plot_in_cell_below=True):
     """
     Visualize a network interactively using Ulf Aslak's d3 web app.
     Saves the network as json, saves the passed config and runs 
     a local HTTP server which then runs the web app.
     
     Parameters
     ----------
-    network : networkx.Graph or networkx.DiGraph
+    network : networkx.Graph or networkx.DiGraph or node-link dictionary
         The network to visualize
     port : int, default : 9853
         The port at which to run the server locally.
@@ -245,7 +246,10 @@ def visualize(network,
     configpath = os.path.join(web_dir, configname)
 
     with open(filepath,'w') as f:
-        json.dump(nx.node_link_data(network), f, iterable_as_array=True)
+        if type(network) is nx.Graph:
+            json.dump(nx.node_link_data(network), f, iterable_as_array=True)
+        else:
+            json.dump(network, f, iterable_as_array=True)
 
     with open(configpath,'w') as f:
         json.dump(this_config, f)
@@ -301,7 +305,7 @@ def visualize(network,
         # apparently this is how it has to be on Windows
         is_jupyter = 'JPY_PARENT_PID' in env
 
-    if is_jupyter and not is_keyboard_interrupted:
+    if is_jupyter and plot_in_cell_below and not is_keyboard_interrupted:
         fig, ax = wulf.draw_netwulf(posted_network_properties)
 
     return posted_network_properties, posted_config

netwulf/tools.py

@@ -144,12 +144,13 @@ def draw_netwulf(network_properties, fig=None, ax=None, figsize=None):
 
     # filter out node positions for links
     width = network_properties['xlim'][1] - network_properties['xlim'][0]
-    pos = { node['id']: np.array([node['x'], node['y']]) for node in network_properties['nodes'] }
+    height = network_properties['ylim'][1] - network_properties['ylim'][0]
+    pos = { node['id']: np.array([node['x'], height - node['y']]) for node in network_properties['nodes'] }
 
     lines = []
     linewidths = []
     for link in network_properties['links']:
-        u, v = link['link']
+        u, v = link['source'], link['target']
         lines.append([ 
             [pos[u][0], pos[v][0]], 
             [pos[u][1], pos[v][1]]
@@ -175,7 +176,7 @@ def draw_netwulf(network_properties, fig=None, ax=None, figsize=None):
     node_colors = []
 
     for node in network_properties['nodes']:
-        XY.append([node['x'], node['y']])
+        XY.append([node['x'], height - node['y']])
         # size has to be given in points**2
         size.append( 2*node['radius'] )
         node_colors.append(node['color'])