layout notes

Software and other source of layout algorithms:

• Cytoscape:
  • hierarchical layout for non-tree graphs: https://github.com/cytoscape/cytoscape-impl/blob/develop/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithmTask.java
  • https://github.com/cytoscape/cytoscape
• Cytoscape.js
  • hierarchical layout for non-tree graphs: https://github.com/cytoscape/cytoscape.js/blob/master/src/extensions/layout/breadthfirst.js
  • has spring layout
  • grid
  • circular
  • multi circular
• Gephi
• Vis.js
• Viz.js
• D3.js
• Three.js
• Sigma.js: https://github.com/jacomyal/sigma.js/
• Graphviz
• Graph-tool
• NetworkX native, AGraph, Graphviz
• IGraph
• Pajek
• Tom Sawyer: https://tomsawyer.com/products/layout/
• R C++ Java
  • JGraph: https://github.com/jgraph/jgraphx
• Articles
  • Graph layout algorithms and libraries: Overview and improvement: http://www.kroki-mde.net/wp-content/uploads/2014/12/VadernaICIST.pdf
  • Spectrum-based networks visualization for topology analysis: http://sci-hub.io/10.1109/mcg.2012.89
  • Spectral methods for analyzing and visualizing networks: an introduction: http://www.sfu.ca/personal/archives/richards/Pages/NAS.AJS-WDR.pdf
• GraphDrawing.org: http://graphdrawing.org/index.html
  • anual symposia
  • electronic archive by topics
  • tutorial with GD systems: http://graphdrawing.org/literature/gd-constraints.pdf
• Mindfusion diagramming: http://mindfusion.eu/graph-layout.html
  • has some unusual layouts such as fractal or composite.
  • did not find source code (I think there isn't any).

Algorithms:

• in Julia: https://github.com/JuliaGraphs/NetworkLayout.jl
  • Has an optimized walker algorithm for trees
  • Algs:
    • Scalable Force Direccted Placament (SFDP), a spring-electric force layout
    • Tree
    • FR
    • Stress majorization
    • Spectral
    • Circular/Shell
• Force:
  • spring:
    • in XSLT: http://graphml.graphdrawing.org/download.html
  • attraction/repulsion: Fruchterman-Reingold, Atlas2
    • spring and electric repulsion: http://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=6297585
• Measure -> ordering:
  • geometric:
    • Versinus
    • Circular:
      • Shell (Multi Circular)
      • Periodic
      • Semi-circular (e.g. spiral)
    • Hive
  • Hierarchical:
    • tree
    • new from tree algorithm
    • cytoscape
    • Coffman-Graham
    • dot
    • from hierarchical measures: https://arxiv.org/pdf/1202.0191.pdf
    • Is Grid layout a HL? Greater measure e.g. degree can be thought as a dominance or hierarchy measure.
• Multilevel:
  • https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3342218/
• Spectral
• Fabric: http://www.biofabric.org/
• Polar (nodeXL): http://www.connectedaction.net/how-to-plot-a-network-in-a-polar-layout-using-nodexl/
• Group in a box (nodeXL): http://www.connectedaction.net/group-in-a-box-a-new-layout-option-in-nodexl-v-164/

other notes

Check the CRI file of ccNetViz.

JS laibraries for numerical computing

• stdlib: https://github.com/stdlib-js/stdlib
• numjs: https://github.com/nicolaspanel/numjs
• furious.js: https://github.com/amd/furious.js/
• https://www.npmjs.com/browse/keyword/numpy
• https://github.com/fernandezajp/PyExtJS
• https://github.com/toji/gl-matrix

ideas

• Make a command line tool which recieves a graph as input and opens the graph in the browser. Maybe make an Ubuntu package.
• ccNetViz only accepts json. It might be easier to write a translation of other graph formats into the accepted json than to translate graphs of interest by hand before loading. Example database of networks:
  • https://snap.stanford.edu/data
  • http://konect.uni-koblenz.de/
  • http://www-personal.umich.edu/~mejn/netdata/