DiffGraph: Visualize the differential graph

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

Visualize the differential graph

Description

Function visualizing the differential graph, i.e., the network of edges that are unique for 2 class-specific graphs over the same vertices

Usage

DiffGraph(
  P1,
  P2,
  lay = "layout_with_fr",
  coords = NULL,
  Vsize = 15,
  Vcex = 1,
  Vcolor = "orangered",
  VBcolor = "darkred",
  VLcolor = "black",
  P1color = "red",
  P2color = "green",
  main = ""
)

Arguments

P1	Sparsified precision matrix for class 1.
P2	Sparsified precision matrix for class 2.
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.
P1color	A character determining the color of edges unique to P1.
P2color	A character determining the color of edges unique to P2.
main	A character giving the main figure title.

Details

Say you have 2 class-specific precision matrices that are estimated over the same variables/features. This function visualizes in a single graph the edges that are unique to the respective classes. Hence, it gives the differential graph. Edges unique to P1 are colored according to P1color. Edges unique to P2 are colored according to P2color. Dashed lines indicate negative precision elements while solid lines indicate positive precision elements.

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.

Value

The function 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.

See Also

Ugraph

Examples

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

## Obtain some (high-dimensional) data, class 2
set.seed(123456)
X2 = matrix(rnorm(n*p), nrow = n, ncol = p)
colnames(X2)[1:25] = letters[1:25]

## Obtain regularized precision under optimal penalty, classes 1 and 2
OPT  <- optPenalty.LOOCV(X, lambdaMin = .5, lambdaMax = 30, step = 100)
OPT2 <- optPenalty.LOOCV(X2, lambdaMin = .5, lambdaMax = 30, step = 100)

## Determine support regularized standardized precision under optimal penalty
PC0  <- sparsify(symm(OPT$optPrec), threshold = "localFDR")$sparseParCor
PC02 <- sparsify(symm(OPT2$optPrec), threshold = "localFDR")$sparseParCor

## Visualize differential graph
DiffGraph(PC0, PC02)

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