A layout algorithm for undirected compound graphs |
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Authors: | Ugur Dogrusoz Erhan Giral Ali Civril |
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Affiliation: | a Computer Engineering Department, Bilkent University, Cankaya, 06800 Ankara, Turkey b Tom Sawyer Software, Oakland, CA, USA c Rensselaer Polytechnic Institute, Troy, NY, USA d Memorial Sloan-Kettering Cancer Center, New York, NY, USA |
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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. |
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Keywords: | Information visualization Graph drawing Force-directed graph layout Compound graphs Bioinformatics |
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