iGraph Python, convert edge list to tuple and add.edges

1
votes

I have a Graph G1 with 50 nodes and 100 edges. All edges are weighted. I have created a list of edges (sorted by a pre-defined order, removing specific edges with large values), and they are indexed like:

Edgelist: [75, 35, 32, 1, ...]

I want to add the edges to a different graph G2 in batches of 10 (to save computation time), but add.edges seems to want a tuple list of vertex pairs. So,

  1. How can I convert the Edge list above into a tuple list, e.g. [(40,2),(10,1),(10,11),(0,0),...]. I've tried a loop with G1.es[edge].tuple, but iGraph reads the [edge] variable as an attribute, whereas if you just write G1.es[75].tuple, it works fine.

  2. How can I look up weights from G1 and add them to G2 in batches of 10?

2
pythonigraphedge-list
Is "Edge List" above a list of edge IDs referring to G1? – Tamás
Yes it is. I have posted below my solution, but maybe there is a way of speeding it up? – user2524828
I have posted a possible implementation below as an answer. – Tamás
Thanks - do you have an R implementation for generating tuples from edge ids? – user2524828
Use get.edgelist() in R to get the full edge list and then simply index the list with the IDs of the edges you are interested in. – Tamás

2 Answers

1
votes

  1. You have to be aware that indexing G1.es with a single number will return an object of type Edge, while indexing it with a list of numbers will return an object of type EdgeSeq. Edge objects have a property named tuple, but EdgeSeq objects don't, so that's why G1.es[edgelist].tuple does not work However, you can do this:

    sorted_tuples = [edge.tuple for edge in G1.es[edgelist]]

    You can also extract the value of the weight attribute directly from the EdgeSeq object:

    sorted_weights = G1.es[edgelist]["weight"]

  2. Here you can make use of the fact that if G2 has M edges and you add m extra edges, then the IDs of these new edges will be in the range from M (inclusive) to M+m (exclusive):

    M = G2.ecount()
m = len(sorted_tuples)
G2.add_edges(sorted_tuples)
G2.es[M:(M+m)] = sorted_weights
0
votes

1) Graph G1 has had unwanted edges deleted already. Edgelist is the edge order for G1.

tuple_list=[]
for e in G1.es:
    tuple_list.append(e.tuple)

sorted_tuples=[tuple_list[i] for i in Edgelist]
sorted_weights = [G1.es['weight'][o] for o in Edgelist]

2) Add edges - this can simply be looped for all edges in G1. Example below for first 10.

edges_to_add=sorted_tuples[0:10]
weights_to_add=sorted_weights[0:10]

G2.add_edges(edges_to_add)

for edge in range(len(edges_to_add)):
    G2.es[G2.get_eid(edges_to_add[edge][0],edges_to_add[edge][1],0)]['weight'] = weights_to_add[edge]

Edge weights are added individually, which is a little slow, but there doesn't seem to be a way of adding edge weights in a batch in iGraph