plotLinkCommDend function

Plot a Coloured Dendrogram of Link Communities

This function is called by plot.linkcomm to plot a dendrogram of coloured link communities.

plotLinkCommDend(x, col = TRUE, pal = brewer.pal(9, "Set1"), 
        height = x$pdmax, right = FALSE, labels = FALSE, plotcut = TRUE, 
        droptrivial = TRUE, leaflab = "none", verbose = TRUE, ...)

Arguments

• x: An object of class linkcomm.
• col: Logical, whether to add community-specific colours. Defaults to TRUE.
• pal: A character vector describing a colour palette to be used for colouring the communites in the dendrogram plot. Defaults to brewer.pal(9, "Set1").
• height: A numerical value specifying the height at which the dendrogram is cut. Defaults to the maximum partition density height.
• right: Logical, whether to orient the dendrogram to the right. Defaults to FALSE.
• labels: Logical, whether to include labels in the dendrogram. Defaults to FALSE.
• plotcut: Logical, whether to display a horizontal line where the dendrogram is cut. Defaults to TRUE.
• droptrivial: Logical, whether to not colour communities of size 2. Defaults to TRUE.
• leaflab: A character string describing the leaf labels on the dendrogram. Can be one of "none", "perpendicular", or "textlike". Defaults to "none".
• verbose: Logical, whether to display the progress of colouring the dendrogram on screen. Defaults to TRUE.
• ...: Additional arguments to be passed to plot.

Details

Here we describe the parameters for plotting coloured dendrograms using:

plot(x, type = "dend")

Returns

A dendrogram plot.

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

Examples

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

## Plot a coloured dendrogram.
plot(lc, type = "dend")