Re: [igraph] appending and coloring nodes

[Ahmed Abdeen Hamed]

Thank you!

It is not liking the headers of the csv files:

Ahmeds-MacBook-Pro:python-projects ahamedCOM$ python file-reader.py 

Traceback (most recent call last):

  File "file-reader.py", line 8, in <module>

    g = Graph.DictList(vertices=None, edges=chain(reader1, reader2))

  File "/Library/Python/2.7/site-packages/igraph/__init__.py", line 2246, in DictList

    v1 = vertex_name_map[edge_data[efk_src]]

KeyError: 'source'

-Ahmed

On Sat, Nov 16, 2013 at 11:32 AM, Tamás Nepusz <address@hidden> wrote:

Hi,

How do you append to a graph from a file?

Here is a scenario of what I am trying to do I have two different csv files:

1. How about concatenating the two files first and then loading the combined file? 

2. If you don’t want to concatenate the physical files, you can still concatenate the CSV reader objects that you use to read them:

from itertools import chain

reader1 = csv.DictReader(open(“file1.csv”))

reader2 = csv.DictReader(open(“file2.csv”))

g = Graph.DictList(vertices=None, edges=chain(reader1, reader2))

3. If you already have a graph and you want to add edges from another file to it, you will need a lookup table that 1) maps vertex names from the first graph to the corresponding vertex IDs, 2) is able to create new IDs for vertex names from the second that it hasn’t seen yet. igraph’s UniqueIdGenerator object can help you with that:

# Create the UniqueIdGenerator and pre-load it with the names from the first graph

id_gen = UniqueIdGenerator()

for name in first_graph.vs[“name”]:

    id_gen.add(name)

# Read the second graph

reader = csv.DictReader(open(“file2.csv”))

new_edges = []

for row in reader:

    new_edges.append(id_gen[row[“source”]], id_gen[row[“target”]])

# Add the new vertices and edges to the graph

n = g.vcount()

if n < len(id_gen):

    g.add_vertices(len(id_gen) - n)

    g.vs[“name”] = id_gen.values()

g.add_edges(new_edges)

I know that it’s a bit cumbersome; the Python interface desperately needs a Graph.union_by_name() function but I haven’t had time to add it yet.

— 

T.

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