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Automatic graph visualization package

Project description

An automatic graph visualize package for `Cytoscape <https://cytoscape.org/>`__.

More Details

Automatic Graph Visualizer[AGVIZ] is one of the Cytoscape Projects. AGVIZ attaches some visualize information for the Cytoscape to the network structure information (CX format).

System Requirements

To use AGVIZ, you need the following:

  • Ubuntu (Recommend >=18.04) or macOS (Recommend >=10.14)
    • Windows is not supported
  • Python 3.x

Installing

Download or clone this repository

$ git clone https://github.com/idekerlab/auto-graph-visualizer

In the downloaded (cloned) directory, install using setup.py

$ python3 setup.py install

Known issues in installing

  • Perhaps, you have some error in python-igraph installation depending on some environments. In such case, try the following installation before setup.

    $ apt install build-essential python3-dev libxml2 libxml2-dev zlib1g-dev
    

    Usage

    $ cat your_file | agviz
    

    Options:

  • -n : Output graph name (.cx). (default : ‘test_out’)

  • -p : Output directory path. (default : ‘./’)

  • -a : Community detection algorithm. (default : ‘greedy’)

    • greedy : Based on the greedy optimization of modularity detail
    • eigenvec : Newman’s eigenvector community structure detection. detail
    • labelprop : The label propagation method of Raghavan et al. detail
    • rest : Community Detection Rest service. detail (github) See the `example <https://github.com/idekerlab/auto-graph-visualizer/blob/master/examples/UsingRestComDetec.ipynb>`__ how to use.
  • -cp : Base color palette. (default : ‘hls’)

    • hls
    • Accent
    • Set1
    • brg
    • hsv
    • gnuplot
  • -ns : The standard of nodesize. (default : ‘betweenness’)

    • closeness
    • degree
    • pagerank
    • betweenness
    • diversity
  • -maxns : Value of criterion which maximum the node size. (default : 100 *you may need adjust this value according to the criterion and the network)

  • -d : Density of output graph.(default : ‘normal’)

    • density
    • normal
    • sparse
  • -pos : Algorithm of node positioning for graph layout.(default : ‘fa’)

    • fa : forceatras2
    • kk : kamada-kawai >Tomihisa Kamada and Satoru Kawai. An Algorithm for Drawing General Undirected Graphs. Information Processing Letters 31:7-15, 1989.
  • -dln : The number of display labels. (default : 20)

Authors

License

This project is licensed under the MIT License - see the LICENSE file for details

Project details


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