Automatic Graph Visualizer (AGVIZ)

An automatic graph visualize package for Cytoscape.

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 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