orderCommunities function

Order Link Communities According to the Dendrogram

This function returns link communities in the same order as in the hierarchical clustering dendrogram.

orderCommunities(x, clusterids = 1:x$numbers[3], verbose = TRUE)

Arguments

• x: An object of class linkcomm.
• clusterids: An integer vector of community IDs. Defaults to all communities.
• verbose: Logical, whether to print progress of the calculation to the screen. Defaults to TRUE.

Details

Ordering link communities according to the dendrogram can aid in visualization when plotting them as a Spencer circle because it minimses crossing over between links.

Returns

A list with the following components: - ordered: A list of integer vectors. These are the ordered communities of links.

• clusids: An integer vector of community IDs in their new order.

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.

Author(s)

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

See Also

plot.linkcomm, plotLinkCommGraph

Examples

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

## Order communities according to the dendrogram.
orderCommunities(lc)