EntOptLayout

Relative entropy optimization based layout plugin
Categories: entropy, layout, optimization, visualization
**EntOptLayout 2.1 is here!<br/> Check the [http://apps.cytoscape.org/apps/entoptlayout#cy-app-releases-tab Release History] for more info!** The goal of this project to implement a graph layout / network visualization algorithm using a recently published relative entropy optimization based method, called Unified Data Representation ([Kovács IA et al. Sci Rep. 2015](https://www.nature.com/articles/srep13786)). If you are using the plugin, **please cite**: *Ágg B, Császár A, Szalay-Bekő M, Veres DV, Mizsei R, Ferdinandy P, Csermely P and Kovács IA (2019) [The EntOptLayout Cytoscape plug-in for the efficient visualization of major protein complexes in protein-protein interaction and signalling networks](https://academic.oup.com/bioinformatics/article/35/21/4490/5475596), Bioinformatics 35(21):4490-4492* Our detailed **Tutorial** on the use of the plugin: [EntOptLayout Tutorial](https://suopte.com/entopt_2_1_tutorial_20200518.pdf) A **video** about the version 2.1: [EntOptLayout Tutorial Video](http://suopte.com/entopt_2_1_tutorial_video.mp4) This is an **open source** project, hosted on SourceForge. You can check the source code and issue support tickets here: https://sourceforge.net/projects/entopt/ Don't hesitate to send any questions, comments or bug reports also to *agg.bence {at} med.semmelweis-univ.hu*. Any feedback from You is most welcomed! Good Luck and Have Fun :)
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2.1

Works with Cytoscape 3.2

Release Notes

- An option to initialize node coordinates with visible positions of Cytoscape nodes has been implemented, thus EntOpt layout optimization could be applied by starting with the resulting node positions of another layout plugin.

2.0

Works with Cytoscape 3.2

Release Notes

- Memory usage was significantly reduced with sparse representation of the adjacency matrix and calculating overlaps on the fly instead of caching overlap matrix. - The implementation of the underlying numeric optimization algorithm has been restructured to improve speed. - Calculating with edge weights taken from a user selectable node column is implemented. - Besides position, width and normalization factor of the nodes can also be optimized to achieve better layouts. - The main diagonal of the adjacency and the overlap matrix now can be ignored or considered twice during the calculations depending on the characteristics of the visualized network. - Data ordering (one dimensional optimization of node positions) is implemented. - The gradual improvements in the quality of the network layout during the optimization process can be followed with the use of the global and componentwise normalized relative entropy values displayed in the network table and a new table dedicated to the various network components. - It is now possible to perform the network visualization on an adjacency matrix raised to the second power by the plugin before the actual layout task is taking place. - An issue preventing small components to be optimized properly has been fixed.

1.1

Works with Cytoscape 3.1

Release Notes

Fixing layout calculation for special graphs with: loops, parallel links, nodes with no links.

1.0

Works with Cytoscape 3.1

Release Notes

Initial version
CYTOSCAPE 3

Version 2.1

License Click here

Released 26 Sep 2017

Works with Cytoscape 3.2

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