plotLinkCommSummComm {linkcomm}

Plot a Summary of the Link Communities

Description

This function is called by plot.linkcomm to plot either connectedness or modularity of individual link communities.

Usage

plotLinkCommSummComm(x, clusterids = 1:x$numbers[3], summary = "conn", 
        pie = FALSE, col = TRUE, pal = brewer.pal(11, "Spectral"), 
        random = FALSE, verbose = TRUE, ...)

Arguments

x

An object of class linkcomm.

clusterids

An integer vector of community IDs. Defaults to all communities.

summary

A character string specifying the community summary. Can be one of "conn", "mod", "ld" for connectedness, modularity, and link densities respectively. Defaults to "conn".

pie

Logical, whether to plot a pie graph. If FALSE, a bar plot is plotted. Defaults to FALSE.

col

Logical, whether to colour each community differently. Defaults to TRUE.

pal

A character vector describing a colour palette to be used for colouring the link communities. Defaults to brewer.pal(11, "Spectral").

random

Logical, whether to randomise the link colours. Defaults to FALSE.

verbose

Logical, whether to print the progress of the calculation to the screen. Defaults to TRUE.

...

Additional arguments to be passed to plot.

Details

Here we describe the parameters for plotting link community summaries using:
plot(x, type = "commsumm", type = "mod")

Value

A bar graph or pie chart.

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 the modularity of the link communities.
plot(lc, type = "commsumm", summary = "mod")