Layout with Circular and Other Non-linear Constraints Using Procrustes Projection

Dwyer, Tim; Robertson, George Croom

doi:10.1007/978-3-642-11805-0_37

Cited by 7 publications

(6 citation statements)

References 16 publications

(28 reference statements)

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“…The approach, however, does not represent cellular components. Other approaches that group nodes in two-dimensional space have been proposed, such as constrained force-directed layout [13], constrained projections [14], hierarchical graph placement [15,16,17] and others [18,19,20,21]. Despite their good performance even for large networks, the cell structure is not taken into consideration in either of those cases.…”

Section: Introductionmentioning

confidence: 99%

CellNetVis: a web tool for visualization of biological networks using force-directed layout constrained by cellular components

Heberle

Carazzolle

Telles

et al. 2017

Preprint

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Background: The advent of "omics" science has brought new perspectives in contemporary biology through the high-throughput analyses of molecular interactions, providing new clues in protein/gene function and in the organization of biological pathways. Biomolecular interaction networks, or graphs, are simple abstract representations where the components of a cell (e.g. proteins, metabolites etc.) are represented by nodes and their interactions are represented by edges. An appropriate visualization of data is crucial for understanding such networks, since pathways are related to functions that occur in specific regions of the cell. The force-directed layout is an important and widely used technique to draw networks according to their topologies. Placing the networks into cellular compartments helps to quickly identify where network elements are located and, more specifically, concentrated. Currently, only a few tools provide the capability of visually organizing networks by cellular compartments. Most of them cannot handle large and dense networks. Even for small networks with hundreds of nodes the available tools are not able to reposition the network while the user is interacting, limiting the visual exploration capability. Results: Here we propose CellNetVis, a web tool to easily display biological networks in a cell diagram employing a constrained force-directed layout algorithm. The tool is freely available and open-source. It was originally designed for networks generated by the Integrated Interactome System and can be used with networks from others databases, like InnateDB. Conclusions: CellNetVis has demonstrated to be applicable for dynamic investigation of complex networks over a consistent representation of a cell on the Web, with capabilities not matched elsewhere.

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Section: Introductionmentioning

confidence: 99%

CellNetVis: a web tool for visualization of biological networks using force-directed layout constrained by cellular components

Heberle

Carazzolle

Telles

et al. 2017

Preprint

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“…Therefore, we decided to first evaluate the simplest of our edge-compression techniques. Layout of the graphs used in the study was accomplished by constrained-force directed layout [10]. We also made some manual fine adjustments to resolve obvious layout issues and maximize readability.…”

Section: Techniquesmentioning

confidence: 99%

Edge Compression Techniques for Visualization of Dense Directed Graphs

Dwyer

Riche

Marriott

et al. 2013

IEEE Trans. Visual. Comput. Graphics

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We explore the effectiveness of visualizing dense directed graphs by replacing individual edges with edges connected to 'modules'-or groups of nodes-such that the new edges imply aggregate connectivity. We only consider techniques that offer a lossless compression: that is, where the entire graph can still be read from the compressed version. The techniques considered are: a simple grouping of nodes with identical neighbor sets; Modular Decomposition which permits internal structure in modules and allows them to be nested; and Power Graph Analysis which further allows edges to cross module boundaries. These techniques all have the same goal--to compress the set of edges that need to be rendered to fully convey connectivity--but each successive relaxation of the module definition permits fewer edges to be drawn in the rendered graph. Each successive technique also, we hypothesize, requires a higher degree of mental effort to interpret. We test this hypothetical trade-off with two studies involving human participants. For Power Graph Analysis we propose a novel optimal technique based on constraint programming. This enables us to explore the parameter space for the technique more precisely than could be achieved with a heuristic. Although applicable to many domains, we are motivated by--and discuss in particular--the application to software dependency analysis.

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“…230-236]. More recently, Dwyer et al [12], [13] explored constrained stress minimization in the presence of geometric constraints useful in interactive graph-drawing and diagramming applications. In this paper, we develop techniques that extend these concepts to provide multidimensional scaling of data points in a deformable mesh onto which the original map imagery is mapped through piecewise-affine transformations.…”

Section: Topology Preserving Multidimensional Scalingmentioning

confidence: 99%

“…4). We can also require minimum height triangles by projection of the triangle of the same base length by solving a simple procrustes problem on the three vertices, following [13]. When using a positive constraint on the minimum triangle height we not only prevent triangles from inverting, but also from collapsing.…”

Section: Preserving Mesh Topologymentioning

confidence: 99%

Visual Encoding of Dissimilarity Data via Topology-Preserving Map Deformation

Bouts

Dwyer

Dykes

et al. 2016

IEEE Trans. Visual. Comput. Graphics

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This is the accepted version of the paper.This version of the publication may differ from the final published version. Abstract-We present an efficient technique for topology-preserving map deformation and apply it to the visualization of dissimilarity data in a geographic context. Map deformation techniques such as value-by-area cartograms are well studied. However, using deformation to highlight (dis)similarity between locations on a map in terms of their underlying data attributes is novel. We also identify an alternative way to represent dissimilarities on a map through the use of visual overlays. These overlays are complementary to deformation techniques and enable us to assess the quality of the deformation as well as to explore the design space of blending the two methods. Finally, we demonstrate how these techniques can be useful in several-quite different-applied contexts: travel-time visualization, social demographics research and understanding energy flowing in a wide-area power-grid. Permanent repository link

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Layout with Circular and Other Non-linear Constraints Using Procrustes Projection

Cited by 7 publications

References 16 publications

CellNetVis: a web tool for visualization of biological networks using force-directed layout constrained by cellular components

CellNetVis: a web tool for visualization of biological networks using force-directed layout constrained by cellular components

Edge Compression Techniques for Visualization of Dense Directed Graphs

Visual Encoding of Dissimilarity Data via Topology-Preserving Map Deformation

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