A multi-dimensional approach to force-directed layouts of large graphs

Gajer, Paweł; Goodrich, Michael T.; Kobourov, Stephen G.

doi:10.1016/j.comgeo.2004.03.014

Cited by 81 publications

(48 citation statements)

References 32 publications

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“…By default NAViGaTOR uses an optimized multi-level force directed layout algorithm, called GRIP (Graph dRawing with Intelligent Placement) [43]. Moreover, nodes can be positioned using a mixture of automatic force-directed layout or by a manual placement.…”

Section: Methodsmentioning

confidence: 99%

Visualization of protein interaction networks: problems and solutions

2013

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BackgroundVisualization concerns the representation of data visually and is an important task in scientific research. Protein-protein interactions (PPI) are discovered using either wet lab techniques, such mass spectrometry, or in silico predictions tools, resulting in large collections of interactions stored in specialized databases. The set of all interactions of an organism forms a protein-protein interaction network (PIN) and is an important tool for studying the behaviour of the cell machinery. Since graphic representation of PINs may highlight important substructures, e.g. protein complexes, visualization is more and more used to study the underlying graph structure of PINs. Although graphs are well known data structures, there are different open problems regarding PINs visualization: the high number of nodes and connections, the heterogeneity of nodes (proteins) and edges (interactions), the possibility to annotate proteins and interactions with biological information extracted by ontologies (e.g. Gene Ontology) that enriches the PINs with semantic information, but complicates their visualization.MethodsIn these last years many software tools for the visualization of PINs have been developed. Initially thought for visualization only, some of them have been successively enriched with new functions for PPI data management and PIN analysis. The paper analyzes the main software tools for PINs visualization considering four main criteria: (i) technology, i.e. availability/license of the software and supported OS (Operating System) platforms; (ii) interoperability, i.e. ability to import/export networks in various formats, ability to export data in a graphic format, extensibility of the system, e.g. through plug-ins; (iii) visualization, i.e. supported layout and rendering algorithms and availability of parallel implementation; (iv) analysis, i.e. availability of network analysis functions, such as clustering or mining of the graph, and the possibility to interact with external databases.ResultsCurrently, many tools are available and it is not easy for the users choosing one of them. Some tools offer sophisticated 2D and 3D network visualization making available many layout algorithms, others tools are more data-oriented and support integration of interaction data coming from different sources and data annotation. Finally, some specialistic tools are dedicated to the analysis of pathways and cellular processes and are oriented toward systems biology studies, where the dynamic aspects of the processes being studied are central.ConclusionA current trend is the deployment of open, extensible visualization tools (e.g. Cytoscape), that may be incrementally enriched by the interactomics community with novel and more powerful functions for PIN analysis, through the development of plug-ins. On the other hand, another emerging trend regards the efficient and parallel implementation of the visualization engine that may provide high interactivity and near real-time response time, as in NAViGaTOR. From a technological point...

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Section: Methodsmentioning

confidence: 99%

Visualization of protein interaction networks: problems and solutions

2013

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“…In the following section, we present a more detailed description of GRIP (Gajer & Kobourov, 2002;Gajer, Goodrich, & Kobourov, 2004), one of the most popular fast force-directed algorithm.…”

Section: Fast Force Directed Drawingmentioning

confidence: 99%

Methods for Multilevel Analysis and Visualisation of Geographical Networks

Rozenblat¹,

Mélançon²

2013

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This Book Series is devoted to examining and solving the major methodological problems social sciences are facing. Take for example the gap between empirical and theoretical research, the explanatory power of models, the relevance of multilevel analysis, the weakness of cumulative knowledge, the role of ordinary knowledge in the research process, or the place which should be reserved to "time, change and history" when explaining social facts. These problems are well known and yet they are seldom treated in depth in scientific literature because of their general nature. So that these problems may be examined and solutions found, the series prompts and fosters the settingup of international multidisciplinary research teams, and it is work by these teams that appears in the Book Series. The series can also host books produced by a single author which follow the same objectives. Proposals for manuscripts and plans for collective books will be carefully examined. The epistemological scope of these methodological problems is obvious and resorting to Philosophy of Science becomes a necessity. The main objective of the Series remains however the methodological solutions that can be applied to the problems in hand. Therefore the books of the Series are closely connected to the research practices.

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“…For instance, along with seminal work on drawing maximal planar graphs [12,20,24] (with triangular outer faces), his work has inspired many researchers to study methods for drawing planar graphs using straight-line edges (e.g., see [1,4,5,6,8,13,17,19]). Moreover, not only has Tutte's result itself been highly influential, but because his method is based on a force-directed layout method, his work has also inspired a considerable amount of work on force-directed layouts (e.g., see [7,9,14,15,21]). …”

Section: Related Prior Workmentioning

confidence: 99%

Drawing Graphs in the Plane with a Prescribed Outer Face and Polynomial Area

Chambers¹,

Eppstein²,

Goodrich³

et al. 2012

JGAA

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We study the classic graph drawing problem of drawing a planar graph using straight-line edges with a prescribed convex polygon as the outer face. Unlike previous algorithms for this problem, which may produce drawings with exponential area, our method produces drawings with polynomial area. In addition, we allow for collinear points on the boundary, provided such vertices do not create overlapping edges. Thus, we solve an open problem of Duncan et al., which, when combined with their work, implies that we can produce a planar straight-line drawing of a combinatorially-embedded genus-g graph with the graph's canonical polygonal schema drawn as a convex polygonal external face. Figure 1. Our problem: given (a) a combinatorially embedded planar graph G and (b) a polygon P with certain vertices on the outer face of G marked as corresponding to vertices of P , find (c) a straight-line embedding of G that uses P as the shape of its outer face.

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A multi-dimensional approach to force-directed layouts of large graphs

Cited by 81 publications

References 32 publications

Visualization of protein interaction networks: problems and solutions

Visualization of protein interaction networks: problems and solutions

Methods for Multilevel Analysis and Visualisation of Geographical Networks

Drawing Graphs in the Plane with a Prescribed Outer Face and Polynomial Area

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