Network visualization: A short introduction to the core concepts of network layout and clustering
Channel: Lars Juhl Jensen
Date: 2021-07-26

A short introduction to the core concepts of network visualization. The presentation provides the minimal overview of the strategies and algorithms to layout, cluster, and simplify networks that can be used to create visualizations of large biological networks (e.g. from STRING) in a network tool such as Cytoscape. You may want to watch my short introduction to the core concepts of network biology first: https://youtu.be/H1bGk8PGvf8

0:00 Introduction: network visualization and why it is hard
0:43 Types of layouts: nodes vs. edges, 2D layouts, force-directed layout, 1D layouts, and circular layout
2:08 Network clustering: dense subgraphs, protein complexes, functional modules, MCL and MCODE algorithms
3:00 Network simplification: less is more, intra-cluster edges, network of clusters, and sorting of 1D layouts
4:20 Positional information: encoding time and subcellular localization