R: Plot a Coloured Dendrogram of Link Communities

plotLinkCommDend {linkcomm}

R Documentation

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 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.

Examples

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

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

[Package linkcomm version 1.0-14 Index]