plot.linkcomm {linkcomm}R Documentation

The linkcomm Plotting Function

Description

This function plots various different linkcomm graphs.

Usage

## S3 method for class 'linkcomm'
plot(x, type = "", ...)

Arguments

x

An object of class linkcomm.

type

A character string specifying the type of plot. Can be one of "summary", "members", "graph", "commsumm", and "dend". See Details below.

...

Additional arguments to be passed to plot.

Details

"summary" plots the dendrogram and partition density plot side-by-side;
"members" plots a community membership matrix;
"graph" plots a graph layout of the network with coloured link communities;
"commsumm" plots a bar graph or pie chart summarising community modularity or connectedness for each community;
"dend" plots a dendrogram with coloured link communities.

See the individual plotting functions for details of arguments that can be passed to plot.linkcomm: plotLinkCommSumm, plotLinkCommMembers, plotLinkCommGraph, plotLinkCommSummComm, and plotLinkCommDend.

Value

Plots to the current device.

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.

See Also

plotLinkCommSumm, plotLinkCommMembers, plotLinkCommGraph, plotLinkCommSummComm, plotLinkCommDend

Examples

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

## Plot a graph of link communities.
plot(lc, type = "graph")
[Package linkcomm version 1.0-14 Index]