# Communities: Search and visualize community-structures In CFWP/rags2ridges: Ridge Estimation of Precision Matrices from High-Dimensional Data

## Description

Function that searches for and visualizes community-structures in graphs.

## Usage

 1 2 3 Communities(P, graph = TRUE, lay = "layout_with_fr", coords = NULL, Vsize = 15, Vcex = 1, Vcolor = "orangered", VBcolor = "darkred", VLcolor = "black", main = "")

## Arguments

 P Sparsified precision matrix graph A logical indicating if the results should be visualized. lay A character mimicking a call to igraph layout functions. Determines the placement of vertices. coords A matrix containing coordinates. Alternative to the lay-argument for determining the placement of vertices. Vsize A numeric determining the vertex size. Vcex A numeric determining the size of the vertex labels. Vcolor A character (scalar or vector) determining the vertex color. VBcolor A character determining the color of the vertex border. VLcolor A character determining the color of the vertex labels. main A character giving the main figure title.

## Details

Communities in a network are groups of vertices (modules) that are densely connected within. Community search is performed by the Girvan-Newman algorithm (Newman and Girvan, 2004).

When graph = TRUE the community structure in the graph is visualized. The default layout is according to the Fruchterman-Reingold algorithm (1991). Most layout functions supported by igraph are supported (the function is partly a wrapper around certain igraph functions). The igraph layouts can be invoked by a character that mimicks a call to a igraph layout functions in the lay argument. When using lay = NULL one can specify the placement of vertices with the coords argument. The row dimension of this matrix should equal the number of vertices. The column dimension then should equal 2 (for 2D layouts) or 3 (for 3D layouts). The coords argument can also be viewed as a convenience argument as it enables one, e.g., to layout a graph according to the coordinates of a previous call to Ugraph. If both the the lay and the coords arguments are not NULL, the lay argument takes precedence. Communities are indicated by color markings.

## Value

An object of class list:

 membership numeric vector indicating, for each vertex, community membership. modularityscore numeric scalar indicating the modularity value of the community structure.

When graph = TRUE the function also returns a graph.

## Author(s)

Carel F.W. Peeters <[email protected]>

## References

Csardi, G. and Nepusz, T. (2006). The igraph software package for complex network research. InterJournal, Complex Systems 1695. http://igraph.sf.net

Fruchterman, T.M.J., and Reingold, E.M. (1991). Graph Drawing by Force-Directed Placement. Software: Practice & Experience, 21: 1129-1164.

Newman, M. and Girvan, M. (2004). Finding and evaluating community structure in networks. Physical Review E, 69: 026113.