A layout algorithm for undirected compound graphs

Ugur Dogrusoz, Erhan Giral, Ahmet Cetintas, Ali Civril, Emek Demir

Research output: Contribution to journalArticlepeer-review

65 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)980-994
Number of pages15
JournalInformation Sciences
Issue number7
StatePublished - Mar 15 2009
Externally publishedYes


  • Bioinformatics
  • Compound graphs
  • Force-directed graph layout
  • Graph drawing
  • Information visualization

ASJC Scopus subject areas

  • Software
  • Control and Systems Engineering
  • Theoretical Computer Science
  • Computer Science Applications
  • Information Systems and Management
  • Artificial Intelligence


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