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| In many cases, biologists are interested in relationship between functional modules first. Then, they look into the details inside the modules, i.e., actual interactions. Cytoscape can partially handle this problem using Group API and some related plugins, | In many cases, biologists are interested in relationship between functional modules first. Then, they look into the details inside the modules, i.e., actual interactions. Cytoscape can partially handle this problem using Group API and some related plugins, but it's not a standard feature. Also, there is no simple file format to represent hierarchy/substructures. |
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| ==== | This is a standard file format in graphviz. It has XML-like structure in the text file, and can represent substructure. |
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| = Unified UI for Module Finding Plugins and New Network Browser = |
==== Pajek ==== This program has 3 types of files to represent substructure: * Partitions – they tell for each vertex to which class vertex belong. Default extension: .clu. * Clusters – subset of vertices (e.g. one class from partition). Default extension: .cls. * Hierarchies – hierarchically ordered vertices. Default extension: .hie. Therefore, user needs to load 4 files (network, partition, cluster, hierarchy) to reconstruct the saved substructures. ==== igraph ==== This package does not have its own file format to represents subgraph. Instead, supporting GraphML and dot. === Cytoscape New File Format for Subgraphs === === User Interface === |
Support for Modules in Cytoscape
Introduction
In many cases, biologists are interested in relationship between functional modules first. Then, they look into the details inside the modules, i.e., actual interactions. Cytoscape can partially handle this problem using Group API and some related plugins, but it's not a standard feature. Also, there is no simple file format to represent hierarchy/substructures.
Usecases
Implementation
File Formats
Most of popular XML graph file formats support hierarchical structure.
DOT
This is a standard file format in graphviz. It has XML-like structure in the text file, and can represent substructure.
Pajek
This program has 3 types of files to represent substructure:
- Partitions – they tell for each vertex to which class vertex belong. Default extension: .clu.
- Clusters – subset of vertices (e.g. one class from partition). Default extension: .cls.
- Hierarchies – hierarchically ordered vertices. Default extension: .hie.
Therefore, user needs to load 4 files (network, partition, cluster, hierarchy) to reconstruct the saved substructures.
igraph
This package does not have its own file format to represents subgraph. Instead, supporting GraphML and dot.
Cytoscape New File Format for Subgraphs