plotLinkCommSummComm function

Plot a Summary of the Link Communities

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

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")

Returns

A bar graph or pie chart.

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.

Author(s)

Alex T. Kalinka alex.t.kalinka@gmail.com

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")