.. _quick_start:

Quick start
============

Commands for a quick working example in the python console:

.. code-block:: python

    import multixrank
    multixrank.Example().write(path="airport")

This generates a working example based on the "airport" multiplex:

.. code-block:: bash

    `-- airport
        |-- bipartite
        |   |-- 1_2.tsv
        |   |-- 1_3.tsv
        |   `-- 2_3.tsv
        |-- config_minimal.yml
        |-- multiplex
        |   |-- 1
        |   |   |-- FR26.tsv
        |   |   |-- FR3.tsv
        |   |   `-- FR7.tsv
        |   |-- 2
        |   |   |-- UK15.tsv
        |   |   |-- UK26.tsv
        |   |   `-- UK3.tsv
        |   `-- 3
        |       |-- G1.tsv
        |       |-- G24.tsv
        |       `-- G6.tsv
        `-- seeds.txt

The minimal configuration file 'config.yml' looks like this.

.. code-block:: bash

    multiplex:
        1:
            layers:
                - multiplex/1/FR26.tsv
                - multiplex/1/FR3.tsv
                - multiplex/1/FR7.tsv
        2:
            layers:
                - multiplex/2/UK15.tsv
                - multiplex/2/UK26.tsv
                - multiplex/2/UK3.tsv
        3:
            layers:
                - multiplex/3/G1.tsv
                - multiplex/3/G24.tsv
                - multiplex/3/G6.tsv
    bipartite:
        bipartite/1_2.tsv:
            source: 1
            target: 2
        bipartite/1_3.tsv:
            source: 1
            target: 3
        bipartite/2_3.tsv:
            source: 2
            target: 3
    seed:
        seeds.txt

.. code-block:: python

    import multixrank
    multixrank_obj = multixrank.Multixrank(config="airport/config_minimal.yml", wdir="airport")
    ranking_df = multixrank_obj.random_walk_rank()
    multixrank_obj.write_ranking(ranking_df, path="output_airport")
    multixrank_obj.to_sif(ranking_df, path="output_airport/airport_seed7_top3.sif", top=3)

This runs the software and writes the results to the output_airport folder:

.. code-block:: bash

    $ ls output_airport/
    airport_seed7_top3.sif  multiplex_1.tsv  multiplex_2.tsv  multiplex_3.tsv

There is a ranking file for each multiplex:

.. code-block:: bash

    $ head -n 4 output_airport/multiplex_1.tsv
    multiplex	node	score
    1	7	0.250002565842259
    1	169	0.0025983048938841304
    1	199	0.0018837852068513332

The SIF file with the sub-network that includes the top 3 nodes can be opened
and visualized in Cytoscape (https://cytoscape.org) as in the following figure:

.. image:: airport.png
   :align: center
   :width: 400