~tfardet/Weighted-directed-clustering_2021

Code for the figures and network generation functions of the 2021 PRR article
correct mouse node names
Add PRR status and rename mouse brain file
Code to generate the networks and figures

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#Weighted directed clustering

#Interpretations and requirements for heterogeneous, inferred, and measured networks

This repository contains the code to generate the figures from the PRR 2021 paper (also on arXiv) by Tanguy Fardet and Anna Levina.

These were generated using NNGT 2.5.1. It can be installed via pip install nngt (code should also work with later versions but breaking changes can happen, in which case you can specify that you want the 2.5.1 version using pip install nngt==2.5.1).

#Generating the networks

The mouse brain (from NeuroData "Mouse_brain_1") and Fediverse (from dataverse) networks are already included in the repository as .el files. However, you can also check the way they were generated by running the scripts in the networks folder.

#Mouse

The generation of the mouse brain requires the allensdk, which has very specific dependencies (also in terms of package versions); therefore, it is highly recommended to install it in a virtual python environment. It also requires version 2.5.2 or higher for NNGT. In case this fails, you can simply use the provided mouse_brain.el.

python -m venv allen
source allen/bin/activate
pip install allensdk
python get_mouse_data.py
deactivate

Then, you can just run generate_mouse_brain.py.

#Fediverse

To generate the Fediverse instance network, first download the files from dataverse and extract them in the networks folder. Then, you can just run generate_fediverse_networks.py.