linkcomm2cytoscape {linkcomm} | 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 |
interaction |
A character string indicating the type of interaction between nodes. Defaults to |
ea |
A character string indicating the file for writing the edge attributes. Defaults to |
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.
## Not run:
linkcomm2cytoscape(lc)
## End(Not run)