A layout algorithm for undirected compound graphs

Authors:
Ugur Dogrusoz;Erhan Giral;Ahmet Cetintas;Ali Civril;Emek Demir
Affiliations:
Computer Engineering Department, Bilkent University, Cankaya, 06800 Ankara, Turkey and Tom Sawyer Software, Oakland, CA, USA;Tom Sawyer Software, Oakland, CA, USA;Computer Engineering Department, Bilkent University, Cankaya, 06800 Ankara, Turkey;Rensselaer Polytechnic Institute, Troy, NY, USA;Memorial Sloan-Kettering Cancer Center, New York, NY, USA
Venue:
Information Sciences: an International Journal
Year:
2009

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Abstract

We present an algorithm for the layout of undirected compound graphs, relaxing restrictions of previously known algorithms in regards to topology and geometry. The algorithm is based on the traditional force-directed layout scheme with extensions to handle multi-level nesting, edges between nodes of arbitrary nesting levels, varying node sizes, and other possible application-specific constraints. Experimental results show that the execution time and quality of the produced drawings with respect to commonly accepted layout criteria are quite satisfactory. The algorithm has also been successfully implemented as part of a pathway integration and analysis toolkit named PATIKA, for drawing complicated biological pathways with compartmental constraints and arbitrary nesting relations to represent molecular complexes and various types of pathway abstractions.