cutDendrogramAt function

Extract Meta-Communities

This function extracts meta-communities from a dendrogram of community relatedness based on a user-defined place at which to cut the dendrogram.

cutDendrogramAt(x, lc = NULL, cutat = NULL, plot = TRUE, col = TRUE, 
                pal = brewer.pal(9, "Set1"), labels = FALSE, plotcut = TRUE, 
                right = TRUE, verbose = TRUE, ...)

Arguments

• x: An object of class hclust, usually generated by getClusterRelatedness.
• lc: An object of class linkcomm. If included, the resulting plot will display additional information about the clusters. Defaults to NULL.
• cutat: A numerical value at which to cut the dendrogram.
• plot: Logical, whether to plot the dendrogram and the meta-communities, defaults to TRUE.
• col: Logical, whether to colour the meta-communites.
• pal: A character vector describing a colour palette to be used for colouring the meta-communites in the dendrogram plot. Defaults to brewer.pal(9, "Set1").
• labels: Logical, whether to put labels on the dendrogram. Defaults to FALSE.
• plotcut: Logical, whether to display a horizontal line where the dendrogram is cut. Defaults to TRUE.
• right: Logical, whether to orient the dendrogram to the right. Defaults to TRUE.
• verbose: Logical, whether to display the progress of colouring the dendrogram. Defaults to TRUE.
• ...: Additional arguments to be passed to plot.

Details

Extracting meta-communities allows the user to explore community relatedness and structure at higher levels.

Returns

A list of integer vectors, referring to meta-communities of link communities.

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

getClusterRelatedness

Examples

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

## Cut dendrogram at 1 and extract meta-communities.
cutDendrogramAt(hc, cutat = 1)