linkcomm2cytoscape function

Write an Edge Attribute File for Cytoscape

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

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).

Returns

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

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.

Author(s)

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

Examples

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

## Write an edge attribute file to disk.
## Not run:

linkcomm2cytoscape(lc)
## End(Not run)