Communities: Search and visualize community-structures

In rags2ridges: Ridge Estimation of Precision Matrices from High-Dimensional Data

Search and visualize community-structures

Description

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

Usage

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 <[e-mail]>

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.

See Also

Ugraph

Examples

## Obtain some (high-dimensional) data
p = 25
n = 10
set.seed(333)
X = matrix(rnorm(n*p), nrow = n, ncol = p)
colnames(X)[1:25] = letters[1:25]

## Obtain regularized precision under optimal penalty
OPT <- optPenalty.LOOCV(X, lambdaMin = .5, lambdaMax = 30, step = 100)

## Determine support regularized standardized precision under optimal penalty
PC0 <- sparsify(symm(OPT$optPrec), threshold = "localFDR")$sparseParCor

## Search and visualize communities
Commy <- Communities(PC0)

rags2ridges documentation built on Oct. 14, 2023, 5:06 p.m.