How to convert a Networkx Graph into an igraph object (from python to R)

2
votes

I have two graph objects made from scratch with Networkx (Python 3.8). To help understanding the situation this is a summary snippet:

G = nx.Graph()
Z = nx.Graph()

#some work here to get data for nodes and edges

G.add_nodes_from([(data["id"], {"origin": data["origin"], "text": data["text"]})])

#some other work in order to hash data for improved nodes privacy

G.add_edge(h.hexdigest(), data["x"])
Z.add_edge(h.hexdigest(), data["x"], weight=polarity) #here polarity is a simple double value

Now, the problem is that I want to export those objects in order to do some work with RStudio and the package igraph. Until now I've tried the following things (without any luck):

  1. Export to a straightforward adjacency list (but in RStudio I get an error, something related to the fact that it expects a square matrix, I don't remember well)
  2. Export to an edge list (but I get another type of error, it seems that i cannot use the weight representation)
  3. Use a naive approach, export in gml format, then install python-igraph, read the gml file with the function Read_Adjacency() and then re-export with the function Write_Adjacency() (hoping that with this intermediate step it somehow make the format understandable by igraph)
  4. I tried the solutions proposed here but also this time without success

How can I do ?

This is the code I use in RStudio:

ADJACENCY=read.csv("myadjlist.csv",header=FALSE,row.names=NULL,sep=";")
ADJACENCY=as.matrix(ADJACENCY)
#then we create the graph
G=graph_from_adjacency_matrix(ADJACENCY, mode="undirected")

And the error:

Error in graph.adjacency.dense(adjmatrix, mode = mode, weighted = weighted, : At structure_generators.c:274 : Non-square matrix, Non-square matrix

This is my adjacency list:

link

1
rpython-3.xgraphnetworkxigraph
Please provide some additional detail. For instance, share the adjacency list you are using and post the specific error you received. If we cannot see the kind of objects involved and the errors, it's hard to give help. - nicola
It looks like as ADJACENCY is actually not an adjacency matrix. Please, share it with dput so we can check it. - nicola
Ok, now I edited - docdev
That file doesn't look like an adjacency list. Did you see it? How should it be interpreted? For instance a row is: 820976985387313;d54fd34cbddc270cafac961fa721b4406cc6de97;1c0e32c2bebad24ad7a06350a909788643ed13aa;ec13d5dd8f9e011e3114bd23404fe1a50da875aa. What is supposed to mean? - nicola
Well, I just used Networkx in python with the function nx.write_adjlist(G, "my csv"). So I expect the output to be an adj list. My interpretation of that line is that node 820976985387313 is connected with d54fd34cbddc270cafac961fa721b4406cc6de97 and so on until the newline character is reached - docdev

1 Answers

1
votes

igraph nowadays support direct conversion from and to networkx objects. See https://igraph.org/python/doc/igraph.Graph-class.html#from_networkx for more details. If you first convert to an igraph object (in Python), write it to a file, and then read it back in using igraph (in R), this should work correctly.