matplotlib renders special *_canvas coordinates; set singleton nodes …

…default true
benmaier · May 17, 2019 · b4bef4a · b4bef4a
1 parent c1d5860
commit b4bef4a
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Showing 2 changed files with 16 additions and 18 deletions.
diff --git a/netwulf/interactive.py b/netwulf/interactive.py
@@ -160,7 +160,7 @@ def log_message(self, format, *args):
     'link_alpha': 0.5,
     'link_width_unevenness': 0.5,
     # Thresholding
-    'display_singleton_nodes': False,
+    'display_singleton_nodes': True,
     'min_link_weight_percentile': 0,
     'max_link_weight_percentile': 100
 }

diff --git a/netwulf/tools.py b/netwulf/tools.py
@@ -10,7 +10,7 @@
 from matplotlib.collections import LineCollection, EllipseCollection
 
 
-def bind_properties_to_network(G,
+def bind_properties_to_network(network,
                                network_properties,
                                bind_node_positions=True,
                                bind_node_color=True,
@@ -21,11 +21,11 @@ def bind_properties_to_network(G,
                                bind_link_color=True,
                                bind_link_alpha=True):
     """
-    Binds properties from the interactive visualization to the `G` object.
+    Binds calculated positional values to the network as node attributes `x` and `y`.
 
     Parameters
     ----------
-    G : networkx.Graph or networkx.DiGraph
+    network : networkx.Graph or something alike
         The network object to which the position should be bound
     network_properties : dict
         The network properties which are returned from the
@@ -48,32 +48,30 @@ def bind_properties_to_network(G,
     if bind_node_positions:
         x = { node['id']: node['x'] for node in network_properties['nodes'] }
         y = { node['id']: node['y'] for node in network_properties['nodes'] }
-        nx.set_node_attributes(G, x, 'x')
-        nx.set_node_attributes(G, y, 'y')
-        G.graph['xlim'] = network_properties['xlim']
-        G.graph['ylim'] = network_properties['ylim']
+        nx.set_node_attributes(network, x, 'x')
+        nx.set_node_attributes(network, y, 'y')
+        network.graph['rescale'] = False
     if bind_node_color:
         color = { node['id']: node['color'] for node in network_properties['nodes'] }
-        nx.set_node_attributes(G, color, 'color')
+        nx.set_node_attributes(network, color, 'color')
     if bind_node_radius:
         radius = { node['id']: node['radius'] for node in network_properties['nodes'] }
-        nx.set_node_attributes(G, radius, 'radius')
+        nx.set_node_attributes(network, radius, 'radius')
 
     # Add individual link attributes
     if bind_link_width:
         width = { (link['source'], link['target']): link['width'] for link in network_properties['links'] }
-        nx.set_edge_attributes(G, width, 'width')
+        nx.set_edge_attributes(network, width, 'width')
 
     # Add global style properties
     if bind_node_stroke_color:
-        G.graph['nodeStrokeColor'] = network_properties['nodeStrokeColor']
+        network.graph['nodeStrokeColor'] = network_properties['nodeStrokeColor']
     if bind_node_stroke_width:
-        G.graph['nodeStrokeWidth'] = network_properties['nodeStrokeWidth']
+        network.graph['nodeStrokeWidth'] = network_properties['nodeStrokeWidth']
     if bind_link_color:
-        G.graph['linkColor'] = network_properties['linkColor']
+        network.graph['linkColor'] = network_properties['linkColor']
     if bind_link_alpha:
-        G.graph['linkAlpha'] = network_properties['linkAlpha']
-
+        network.graph['linkAlpha'] = network_properties['linkAlpha']
 
 def get_filtered_network(network,edge_weight_key=None,node_group_key=None):
     """
@@ -193,7 +191,7 @@ 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]
     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'] }
+    pos = { node['id']: np.array([node['x_canvas'], height - node['y_canvas']]) for node in network_properties['nodes'] }
 
     lines = []
     linewidths = []
@@ -224,7 +222,7 @@ def draw_netwulf(network_properties, fig=None, ax=None, figsize=None):
     node_colors = []
 
     for node in network_properties['nodes']:
-        XY.append([node['x'], height - node['y']])
+        XY.append([node['x_canvas'], height - node['y_canvas']])
         # size has to be given in points*2
         size.append( 2*node['radius'] )
         node_colors.append(node['color'])