I have 20 directed graphs in grap-tool (Python 3.4) and all have the same node name (it is an attribute, called 'name'), but vary in terms of connections and attributes.
I am trying to plot those networks across time (i.e., how the edges changed at every timestep, and how the attributes such as color changed). For that, I need to fix the position of the nodes for all plots.
I tried this:
import graph_tool.all as gt
## networks = {dictionary of time as the key and the Graph as the value}
#getting the positions of the nodes once that should be fixed across Graphs
initial_pos = gt.arf_layout(networks[0],weight=None, d=0.5,
a=10, dt=0.001, epsilon=1e-06, max_iter=100, pos=None, dim=2)
for round_id in range(0,20):
G = networks[round_id]
fixed_pos = gt.arf_layout(G, max_iter=0, pos=initial_pos)
deg = G.degree_property_map("in")
deg.a = 15 * deg.a + 25
gt.graph_draw(
G,
#pos=fixed_pos,
vertex_fill_color=G.vertex_properties["color"],
vertex_font_size=18,
vertex_size = deg,
vertex_shape = G.vertex_properties["shape"],
edge_pen_width = 5,
output_size=(1000, 1000),
output=("{0}.pdf".format(round_id))
)
but this gives me the following error:
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
<ipython-input-68-4efd39b32b83> in <module>()
5 #f, ax = plt.subplots(nrows=1, ncols=1, figsize=(17, 10), sharex=True)
6 G = nx2gt(networks[round_id])
----> 7 fixed_pos = gt.arf_layout(G, max_iter=0, pos=initial_pos)
8 deg = G.degree_property_map("in")
9 deg.a = 15 * deg.a + 25
/Users/amaatouq/anaconda/lib/python3.4/site-packages/graph_tool/draw/__init__.py in arf_layout(g, weight, d, a, dt, epsilon, max_iter, pos, dim)
393
394 ug = GraphView(g, directed=False)
--> 395 libgraph_tool_layout.arf_layout(ug._Graph__graph, _prop("v", g, pos),
396 _prop("e", g, weight), d, a, dt, max_iter,
397 epsilon, dim)
/Users/amaatouq/anaconda/lib/python3.4/site-packages/graph_tool/__init__.py in _prop(t, g, prop)
177 raise ValueError("Expected '%s' property map, got '%s'" %
178 (names[t], names[prop.key_type()]))
--> 179 return pmap._get_any()
180
181
/Users/amaatouq/anaconda/lib/python3.4/site-packages/graph_tool/__init__.py in _get_any(self)
389 g = self.get_graph()
390 if t == "v":
--> 391 N = g.num_vertices(True)
392 elif t == "e":
393 N = g.edge_index_range
AttributeError: 'NoneType' object has no attribute 'num_vertices'
