cartoGRAPHs 1.0.0

A Network Layout and Visualization Package

CARTOGRAPHS

Visual Network Exploration in two and three dimensions

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Networks offer an intuitive visual representation of complex systems. Important network characteristics can often be recognized by eye and, in turn, patterns that stand out visually often have a meaningful interpretation. However, conventional network layouts are difficult to interpret, as they offer no direct connection between node position and network structure. Here, we propose an approach for directly encoding arbitrary structural or functional network characteristics into node positions. We introduce a series of two and three-dimensional layouts, benchmark their efficiency for model networks, and demonstrate their power for elucidating structure to function relationships in large-scale biological networks.

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ABOUT CARTOGRAPHS

CartoGRAPHs is a python package to generate two- and three-dimensional layouts of networks. Here you will find Jupyter Notebooks to use our method of visualizing different network characteristics based on feature modulation and dimensionality reduction.

To get a first glance on the framework, we provide a Quickstarter Notebook with an examplary graph. Additionally one can dive deeper into real world networks focusing on the Protein Protein Interaction Network.

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NETWORK LAYOUTS

The Network Layouts are themed based on different characteristics of a Network. Those can be of structural or functional nature. Additionally we came up with a method to modulate between both, structural and functional features (please find a "hands-on" example in the Notebook "cartoGRAPHs_FeatureModulation.ipynb").

An Overview on the layouts included within the framework:

• local layout > based on node pairwise adjacencies
• global layout > based on network propagation
• importance layout > based on network centrality metrics, such as degree, closeness, betweenness and eigenvector centrality
• functional layout > e.g. based on a NxM matrix including N nodes in the network and M features
• combined layouts > based on modulation between structural and functional features

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NETWORK CATEGORIES

To experiment with a diversity of two- and three-dimensional visualizations, we came up with four different Layout Categories, named after their natural appearance.

• 2D Network portrait
• 3D Network portrait
• 3D Topographic Network Map
• 3D Geodesic Network Map

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HOW TO CREATE NETWORK VISUALIZATIONS

Check out the provided Jupyter Notebooks in our github repository : https://github.com/menchelab/CartoGRAPHs

Quickstarter | cartoGRAPHs_AQuickStarter.ipynb The Quickstarter Notebook contains basic functions to get familiar with the framework and test different layouts quickly using small network models.

More Detailed Example | cartoGRAPHs_ExemplaryNotebook.ipynb

Focus: Feature Modulation | cartoGRAPHs_FeatureModulation.ipynb

A Biological Network: Human PPI | cartoGRAPHs_ManuscriptFigure.ipynb*