A layout algorithm for undirected compound graphs

Quality of the produced drawings with respect to commonly accepted layout criteria are quite satisfactory. The algorithm has also been successfully implemented as improved, tions do not enforce a hierarchy) but still has structural properties, like symmetry, or includes parts or substructures, 0020-0255/$ - see front matter C211 2008 Elsevier Inc. All rights reserved. q A short demo version of this paper appeared in Proc. of 12th Intl. Symposium on Graph Drawing, NYC, New York, pp. 442–447,

September 29–October 2, 2004. Research supported in part by TUBITAK (The Scientific and Technological Research Council of Turkey), grant number 104E049. * Corresponding author. Address: Computer Engineering Department, Bilkent University, Cankaya, 06800 Ankara, Turkey. Tel.: +90 (312) 290 1612; fax: +90 (312) 266 4047. E-mail address: ugur@cs.bilkent.edu.tr (U. Dogrusoz). Information Sciences 179 (2009) 980–994 Contents lists available at ScienceDirect Information Sciences journal homepage: www.elsevier.com/locate/ins doi:10.1016/j.ins.2008.11.017 interactive graph editing and diagramming facilities have become important components in visualization systems [7]. Effec- tive analysis of the underlying data in graph visualization is only possible with the sound automatic layout capabilities of such systems. The notion of compound graphs has been used, in the past, to represent more complex types of relationships or varying levels of abstractions in data (see Figs. 1 and 2) [20,17,16,14]. There has been a great deal of work done on general graph layout [4] but considerably less on the layout of com- pound graphs, probably due to the difficult nature of the problem. Straightforward approaches to laying out compound graphs in a top-down or bottom-up manner (with respect to the inclusion or nesting hierarchy) fail, due to bidirectional dependencies (e.g., inter-graph edges) between levels of varying depth. The limited work on compound graph layout has mostly focused on the layout of hierarchical graphs [19,18,9], in which the underlying relational information is assumed to be under a certain hierarchy. However, such algorithms perform poorly if the graph is undirected (if the edge direc- Keywords: Information visualization Graph drawing Force-directed graph layout Compound graphs Bioinformatics 1. Introduction As graphical user interfaces have part of a pathway integration and analysis toolkit named PATIKA, for drawing complicated biological pathways with compartmental constraints and arbitrary nesting relations to rep- resent molecular complexes and various types of pathway abstractions. C211 2008 Elsevier Inc. All rights reserved. and more state-of-the-art software tools have incorporated visual functions, A layout algorithm for undirected compound graphs q Ugur Dogrusoz a,b, * , Erhan Giral b , Ahmet Cetintas a , Ali Civril c , Emek Demir d 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 article info Article history: Received 7 May 2008 Received in revised form 5 November 2008 Accepted 10 November 2008 abstract We present an algorithm for the layout of...

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