Community Detection App for Cytoscape

Community Detection App is a Cytoscape App that leverages third party algorithms (via REST service) to perform hierarchical clustering/community detection on a given network. Leveraging the REST service allows incorporation of algorithms not easily portable/distributable with this App. In addition, this tool offers for biologists Term Mapping/Enrichment (also via service) on the hierarchies generated by this App.

NOTE: This service is experimental. The interface is subject to change.

If you use Community Detection App or REST Service in your research, please cite:

Singhal A, Cao S, Churas C, Pratt D, Fortunato S, Zheng F, et al. (2020) Multiscale community detection in Cytoscape. PLoS Comput Biol 16(10): e1008239. https://doi.org/10.1371/journal.pcbi.1008239

Requirements to use

• Cytoscape 3.7 or above
• Internet connection to allow App to connect to remote services

Installation via from Cytoscape

CDAPS is in the Cytoscape App Store and can be installed by following these instructions

Requirements to build (for developers)

• Java 8+ with jdk
• Maven 3.4 or above

To build documentation

• Make
• Python 3+
• Sphinx (install via pip install sphinx)
• Sphinx rtd theme (install via pip install sphinx_rtd_theme)

Building manually

Commands below assume Git command line tools have been installed

# Can also just download repo and unzip it
git clone https://github.com/cytoscape/cy-community-detection

cd cy-community-detection
mvn clean test install

The above command will create a jar file under target/ named cy-community-detection-<VERSION>.jar that can be installed into Cytoscape

Open Cytoscape and follow instructions here and click on Install from File... button to load the jar created above.

Building documentation

Documentation is stored under docs/ directory and uses Sphinx & Python to generate documentation that is auto uploaded from master branch to Read the Docs

# The clone and directory change can be
# omitted if done above
git clone https://github.com/cytoscape/cy-community-detection

cd cy-community-detection
make docs

Once make docs is run the documentation should automatically be displayed in default browser, but if not open docs/_build/html/index.html in a web browser

To add dropshadow and border to images, Image Magick has been used with the following command:

convert foo.png -shave 1x1 -bordercolor black -border 1 \
        ( +clone -background gray -shadow 80x3+5+5 ) +swap \
        -background none -layers merge +repage foo_fixed.png

COPYRIGHT AND LICENSE

Click here

Acknowledgements

• TODO denote funding sources