Fully interactive, dependency-free 3D visualization of multilayered networks.
Arena3Dweb is a web application built with R/Shiny and JavaScript for visualizing multilayered graphs in 3D space, without external dependencies. Integrate multiple networks into a single scene, explore intra- and inter-layer connections, and manipulate the view in real time, including VR mode.
- Multi-layer integration: Load and combine multiple network layers with cross-layer edges.
- 3D Interactivity: Translate, rotate, and scale the scene or individual layers; VR mode supported.
- Rich layouts & clustering: Apply and customize layouts (force-directed, circular, grid) and clustering algorithms on selected layers.
- Dynamic styling: Adjust node size, color, and edge colors on-the-fly to highlight important paths or topological features.
- Themes & export: Choose from three premade themes; export/import sessions in JSON; download high-resolution snapshots.
- Graph support: Handle weighted/unweighted, directed/undirected, and multi-channel graphs up to 10,000 edges (online); unlimited locally.
- API access: Open networks directly from external applications via REST endpoint.
Access the live app at: https://www.arena3d.org
# Pull the Docker image
docker pull pavlopouloslab/arena3dweb
# Run the container (port 3838)
docker run -p 3838:3838 pavlopouloslab/arena3dweb-
Clone the repo:
git clone https://github.com/PavlopoulosLab/Arena3Dweb.git cd Arena3Dweb
2. Install R (>=4.0) and RStudio.
3. Install required R packages:
```r
install.packages(c(
"shiny", "shinyjs", "shinythemes",
"igraph", "RColorBrewer",
"jsonlite", "tidyr"
))
- Open Arena3Dweb.Rproj in RStudio.
- Open server.R, select Run External, then click Run App.
Find downloadable example files in the www/data/ folder:
- TSV files for "Upload Network" format
- JSON files for "Load Session" format
- Upload network files or load a saved session.
- Select layers to apply layouts or clustering.
- Interact with the 3D scene: pan, zoom, rotate, enter VR.
- Customize node/edge styling and themes.
- Export snapshots or session JSON for later reuse.
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Arena3Dweb: interactive 3D visualization of multilayered networks Karatzas E., Baltoumas F.A., Panayiotou N.A., Schneider R., Pavlopoulos G.A. Nucleic Acids Research, 2021;49(W1):W36–W45. doi: 10.1093/nar/gkab278
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Arena3Dweb: interactive 3D visualization of multilayered networks supporting multiple directional information channels, clustering analysis and application integration Kokoli M., Karatzas E., Baltoumas F.A., Schneider R., Pafilis E., Paragkamian S., Doncheva N.T., Jensen L.J., Pavlopoulos G.A. NAR Genomics and Bioinformatics, 2022;5(2):lqad053. doi: 10.1093/nargab/lqad053
This project is released under the MIT License. See LICENSE for details.