Authors:
Jyh-Jong Tsay
1
;
Bo-Liang Wu
2
and
Guo-Gen Huang
2
Affiliations:
1
National Chung Cheng University, Taiwan
;
2
National Chung-Cheng University, Taiwan
Keyword(s):
Pathway layout, Forced-directed layout, Hierarchical layout, Pathway visualization.
Related
Ontology
Subjects/Areas/Topics:
Artificial Intelligence
;
Bioinformatics
;
Biomedical Engineering
;
Soft Computing
;
Visualization
Abstract:
Many complex pathways are described as hierarchical structures in which a pathway is recursively partitioned into several sub-pathways, and organized hierarchically as a tree. The hierarchical structure provides a natural way to visualize the global structure of a complex pathway. Recently, a hierarchically organized layout algorithm HOLY which takes the advantages of the hierarchical structures inherent in complex pathways has been proposed. In this paper, we present a new layout algorithm HOLY-II which follows the basic principle of HOLY, but improves HOLY by introducing a new algorithm for joining layouts, one of the crucial tasks in HOLY. Experiment shows that HOLY-II is able to produce layouts which clearly render both the global structures and the local structures of complex pathways, and gives better visualization for many examples from MetaCyc, CADLIVE and HOLY.