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Last data update: 2014.03.03

R: Write an Edge Attribute File for Cytoscape

linkcomm2cytoscape

R Documentation

Write an Edge Attribute File for Cytoscape

Description

This function writes out an edge attribute file for visualising the link communities in Cytoscape.

Usage

linkcomm2cytoscape(x, interaction = "pp", ea = "temp.ea")

Arguments

`x`	An object of class `linkcomm`.
`interaction`	A character string indicating the type of interaction between nodes. Defaults to `"pp"` for protein-protein interaction.
`ea`	A character string indicating the file for writing the edge attributes. Defaults to `"temp.ea"`.

Details

Cytoscape is an open source platform for complex-network analysis and visualization (Shannon et al. 2003).

Value

Used for its side-effect of writing an edge attribute file to disk.

Author(s)

Alex T. Kalinka alex.t.kalinka@gmail.com

References

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.

Examples

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

## Write an edge attribute file to disk.
linkcomm2cytoscape(lc)