pandas - reshape dataframe to edge list according to column values

Question

Starting from this simple dataframe:

  node   t1   t2
0    a  pos  neg
1    b  neg  neg
2    c  neg  neg
3    d  pos  neg
4    e  neg  pos
5    f  pos  neg
6    g  neg  pos

I would like to build an edgelist file to read it as a undirected network. The expected output is:

b c
a d
a f
d f
e g

So basically I'm linking two nodes if they have the same pair of values in the ['t1','t2'] columns. So far I tried first to group the values into one new column:

d['c'] = [tuple(i) for i in df[['t1','t2']].values]

But then I'm stucked in grouping the users as I wish.

EDIT: fix error in the creation of the new column.

Kirell · Accepted Answer · 2016-01-29 19:13:17Z

3

Have a look at this:

df = pd.DataFrame({'node': ['a', 'b','c', 'd', 'e', 'f', 'g'],
               't1': ['pos', 'neg', 'neg', 'pos', 'neg', 'pos', 'neg'],
               't2': ['neg', 'neg', 'neg', 'neg', 'pos', 'neg', 'pos']})

K = nx.Graph()
K.add_nodes_from(df['node'].values)

# Create edges
for i, group in df.groupby(['t1', 't2'])['node']:
    # generate all combinations without replacement 
    # from the group of similar column pairs
    for u, v in itertools.combinations(group, 2):           
        K.add_edge(u, v)

print(K.edges())

Result: [('a', 'd'), ('a', 'f'), ('c', 'b'), ('e', 'g'), ('d', 'f')]

The trick here is to group by the 2 columns at the same time in pandas. Then, you can just create all combinations of edges to add in the graph.

edited Jan 29, 2016 at 19:13

answered Jan 29, 2016 at 16:34

Kirell

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