plotLinkCommDend {linkcomm}

Plot a Coloured Dendrogram of Link Communities

Description

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

Usage

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")

Value

A dendrogram plot.

Author(s)

Alex T. Kalinka [e-mail]

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.

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")