Metadata-Version: 1.1
Name: auto-graph-visualizer
Version: 0.1.1
Summary: Automatic graph visualization package
Home-page: https://github.com/idekerlab/auto-graph-visualizer
Author: Mikio Shiga, Atsuya Matsubara
Author-email: m-shiga@ist.osaka-u.ac.jp, at-matbr@ist.osaka-u.ac.jp
License: UNKNOWN
Description: Automatic Graph Visualizer (AGVIZ)
        ==================================
        
        **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 <https://home.ndexbio.org/data-model/>`__).
        
        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
        
           .. rubric:: Usage
              :name: 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 <https://journals.aps.org/pre/abstract/10.1103/PhysRevE.70.066111>`__
           -  eigenvec : Newman's eigenvector community structure detection.
              `detail <https://journals.aps.org/pre/abstract/10.1103/PhysRevE.74.036104>`__
           -  labelprop : The label propagation method of Raghavan et al.
              `detail <https://journals.aps.org/pre/abstract/10.1103/PhysRevE.76.036106>`__
           -  rest : Community Detection Rest service.
              `detail <http://ddot.ucsd.edu/cd/>`__
              (`github <https://github.com/ndexbio/communitydetection-rest-server>`__)
              **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 <https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0098679>`__
           -  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 <https://github.com/keiono>`__)
        -  **Atsuya Matsubara** (`Github <https://github.com/ray0bump0>`__)
        -  **Mikio Shiga** (`Github <https://github.com/agis09>`__)
        
        License
        -------
        
        This project is licensed under the MIT License - see the
        `LICENSE <LICENSE>`__ file for details
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: Natural Language :: English
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Programming Language :: Python :: Implementation :: PyPy
