Parens for Python - Network Analysis and Visualization

with IGraph and Lieden

We are going to explore some more Python libraries through the use of libpython-clj.

This time, we are going to look at IGraph and Lieden.

{:deps

 {org.clojure/clojure {:mvn/version "1.10.1"}

  cnuernber/libpython-clj {:mvn/version "1.36"}}}

Install the python dependencies and display

sudo apt-get update

sudo apt-get install eog

conda install -c conda-forge python-igraph cairocffi leidenalg

IGraph

IGraph is a library for network analysis and visualization.

Here we use python require to load it in as well as its supporting plotting library cario.

We then create a graph and add some vertices and edges to it.

(require '[libpython-clj.require :refer [require-python]]

         '[libpython-clj.python :as py :refer [py. py.. py.-]])

(require-python '[igraph :as igraph])

(require-python '[cairocffi])

(def g (igraph/Graph))

(py. g add_vertices 3)

(py. g add_edges [[0 1] [1 2]])

From there we, can continue to add edges and vertices using a interop doto for the graphics. Finally, we can print out a summary of the graph.

(doto g

  (py. add_edges [[2 0]])

  (py. add_vertices 3)

  (py. add_edges [[2 3] [3 4] [4 5] [5 3]]))

(igraph/summary g)

Let's get a more interesting graph using one of the preloaded "Famous" petersen graph and we can plot what it looks like.

(def g2 (py. (igraph/Graph) Famous "petersen"))

(igraph/plot g2, "results/test.png")

0.2s

Clj & Python env (Clojure)

Clojure

Vector(4) [libpython_clj.python.bridge$generic_python_as_jvm$reify__27963, "0x12aa502e", "<igraph.drawing.Plot object at 0x7f8e20147a90>", Map]

Leidenalg

The leindenalg library provides clustering and community detection with graphs. The core function is find_partition which finds the optimal partition using the Leiden algorithm 

(require-python '[leidenalg :as la])

(def G (py. (igraph/Graph) Famous "Zachary"))

;;;Now detecting communities with modularity is straightforward

(def la-partition (la/find_partition G la/ModularityVertexPartition))

(igraph/plot la-partition, "results/partition.png")

0.2s

Clj & Python env (Clojure)

Clojure

Vector(4) [libpython_clj.python.bridge$generic_python_as_jvm$reify__27963, "0x30ee998c", "<igraph.drawing.Plot object at 0x7f8ded90a550>", Map]