A Structural Approach to Disentangle the Visualization of Bipartite Biological Networks

Abstract

Interactions between two different guilds of entities are pervasive in biology. They may happen at molecular level, like in a diseasome, or amongst individuals linked by biotic relationships, such as mutualism or parasitism. These sets of interactions are complex bipartite networks. Visualization is a powerful tool to explore and analyze them, but the most common plots, the bipartite graph and the interaction matrix, become rather confusing when working with real biological networks. We have developed two new types of visualization which exploit the structural properties of these networks to improve readability. A technique called k-core decomposition identifies groups of nodes that share connectivity properties. With the results of this analysis it is possible to build a plot based on information reduction (polar plot) and another which takes the groups as elementary blocks for spatial distribution (ziggurat plot). We describe the applications of both plots and the software to create them.