plotLinkCommMembers {linkcomm}

Plot a Community Membership Matrix for Link Communities

Description

This function is called by plot.linkcomm to plot a community membership matrix for the link communities.

Usage

plotLinkCommMembers(x, nodes = head(names(x$numclusters), 10), 
        pal = brewer.pal(11, "Spectral"), shape = "rect", total = TRUE, 
        fontsize = 11, nspace = 3.5, maxclusters = 20)

Arguments

x

An object of class linkcomm.

nodes

A character vector specifying the node names that will be included in the plot. Defaults to the 10 nodes that belong to the most communities.

pal

A character vector describing a colour palette to be used for community-specific colouring. Defaults to brewer.pal(11, "Spectral").

shape

A character string specifying the shape of matrix entries. Can be one of "rect" or "circle". Defaults to "rect".

total

Logical, whether to display the number of communities each node belongs to and the number of nodes in each community. Defaults to TRUE.

fontsize

A numerical value specifying font size for the node names. Defaults to 11.

nspace

A numerical value specifying how much space to leave at the left for fitting in node names. Defaults to 3.5.

maxclusters

An integer value specifying the maximum number of communities to display. Defaults to 20.

Value

A community membership matrix 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 community membership matrix.
plot(lc, type = "members")