Quick start

Commands for a quick working example in the python console:

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

This generates a working example based on the “airport” multiplex:

`-- 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.

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

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:

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

There is a ranking file for each multiplex:

$ 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:

../../_images/airport.png