auto-graph-visualizer 0.1.1

Automatic graph visualization package

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

• Keiichiro Ono (Github)
• Atsuya Matsubara (Github)
• Mikio Shiga (Github)

License

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