Arena3Dweb: Interactive 3D visualization of multilayered networks supporting multiple directional information channels, clustering analysis and application integration

Maria Kokoli; Evangelos Karatzas; Fotis A. Baltoumas; Reinhard Schneider; Evangelos Pafilis; Savvas Paragkamian; Nadezhda T. Doncheva; Lars Juhl Jensen; Georgios A. Pavlopoulos

doi:10.1101/2022.10.01.510435

ABSTRACT

Arena3D^web is an interactive web tool that visualizes multi-layered networks in 3D space. In this update, Arena3D^web supports directed networks as well as up to nine different types of connections between pairs of nodes with the use of Bézier curves. It comes with different color schemes (light/gray/dark mode), custom channel coloring, four node clustering algorithms which one can run on-the-fly, visualization in VR mode and predefined layer layouts (zig-zag, star and cube). This update also includes enhanced navigation controls (mouse orbit controls, layer dragging and layer/node selection), while its newly developed API allows integration with external applications as well as saving and loading of sessions in JSON format. Finally, a dedicated Cytoscape app has been developed, through which users can automatically send their 2D networks from Cytoscape to Arena3D^web for 3D multi-layer visualization. Arena3D^web is accessible at http://arena3d.pavlopouloslab.info or http://arena3d.org

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

↵& The authors wish to be known that the first two authors should be regarded as joint First Authors
Section "Integration with Cytoscape" rephrased
http://arena3d.org

The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.