linkcomm2clustnsee {linkcomm}

Write a Partition File for Clust&See

Description

This function writes out a partition file which can be imported into the Cytoscape plug-in Clust&See.

Usage

linkcomm2clustnsee(x, file = "temp.cns", network.name = NULL)

Arguments

x

An object of class linkcomm or OCG.

file

A character string naming a Clust&See partition file (.cns extension). Defaults to "temp.cns".

network.name

A character string providing a name for the network. This name must correspond to the file name of the network that will be imported into Cytoscape. If NULL, the object name, x, is used. Defaults to NULL.

Details

Cytoscape is an open source platform for complex-network analysis and visualization, and Clust&See (Spinelli et al. 2013) is a Cytoscape plug-in used for visualizing and manipulating the clusters produced by various network clustering algorithms.

Value

Used for its side-effect of writing a Clust&See partition file to disk.

Author(s)

Alex T. Kalinka [e-mail]

References

Becker, E. et al. (2012) Multifunctional proteins revealed by overlapping clustering in protein interaction network. Bioinformatics 28, 84-90.

Gambette, P. and Guenoche, A. (2011) Bootstrap clustering for graph partitioning. RAIRO-Operations Research 45, 339-352.

Kalinka, A.T. and Tomancak, P. (2011). linkcomm: an R package for the generation, visualization, and analysis of link communities in networks of arbitrary size and type. Bioinformatics 27, 2011-2012.

Shannon, P. et al. (2003) Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Research 13, 2498-2504.

Spinelli, L. et al. (2013) Clust&See: a Cytoscape plugin for the identification, visualization, and manipulation of network clusters. BioSystems 113, 91-95.

Examples

## Generate graph and extract link communities.
g <- swiss[,3:4]
lc <- getLinkCommunities(g)

## Write a partition file to disk.
## Not run: 
linkcomm2clustnsee(lc)

## End(Not run)