nezzle

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Introduction

• Nezzle is an interactive and programmable network visualization software.
• Nezzle was initially developed to visualize biological networks such as signaling networks.
• Nezzle repesents Net + Puzzle, because adjusting nodes and edges of a network for visualization is similar to doing a puzzle.
• Find helpful tutorials in Nezzle's YouTube channel :tv:

Features

• Lightweight, programmable, detailed visualization of complex networks for high quality figures.
• Highly customizable visualization of networks with user-defined source codes.
• Easy and efficient plug-in development enabled by powerful Python ecosystem.
• Manual curation of the positions of nodes and edges by adjusting the graphics in GUI.
• Interactive programming to modify both data and graphics of networks in the GUI console.
• The GUI depends on Python bindings for Qt such as PyQt (abstracted by QtPy in this project).

Installation

:snake: Anaconda is recommended to use and develop Nezzle.

:warning: Apple M1 users are encouraged to use Rosetta Terminal.

Anaconda virtual environment

After installing anaconda, create a conda virtual environment for Nezzle. In the following command, you can change the Python version (e.g.,python=3.7 or python=3.9).

conda create -n nezzle python=3.8

Now, we can activate our virtual environment for Nezzle as follows.

conda activate nezzle

Install pip for installing the dependencies.

conda install pip

Dependency

Check packages and versions in requirements or requirements for conda.

We can install all the dependencies using pip with -r option.

pip install -r requirements.txt

We can also install the dependencies using conda with --file option.

conda install -y --file requirements_conda.txt

Install from PyPI

The simplest way to install Nezzle is using pip.

pip install nezzle

However, the installed package with pip do not contain the examples. To explore the examples, install from this GitHub repository.

Install from GitHub repository

First, clone the recent version of this repository.

git clone https://github.com/dwgoon/nezzle.git nezzle

Now, we need to install Nezzle as a module.

cd nezzle
pip install -r requirements.txt
python setup.py install

Execution

In a terminal, we can just type "nezzle" that is in the "Scripts" sub-directory of a Python environment.

nezzle

Alternatively, we can execute the program in the local repository as follows.

python nezzle.py

Examples

Mapping dynamics data to graphics

Finding suboptimal positions by maximizing mean pairwise distances (PyTorch)

Original network before messing up the layout

Iris dataset layout dynamics (scikit-learn + PyTorch)

Principal component view of Iris dataset

Adjusting network graphics through GUI

Adjusting network graphics by programming with REPL

Creating network graphics by running a code

:computer::keyboard::computer_mouse: More examples

Citation

D. Lee Nezzle: an interactive and programmable visualization of biological networks in Python Bioinformatics 38(12) 3310–3311 (2022).