DEGraph (version 1.24.0)

writeAdjacencyMatrix2KGML: Writes an adjacency matrix into an XML file

Description

Writes an adjacency matrix into an XML file.

Usage

writeAdjacencyMatrix2KGML(mat, pathname, nodePrefix="n", overwrite=FALSE, ..., verbose=FALSE)

Arguments

mat

A matrix, interpreted of the adjacency matrix of a graph.

pathname

The full path name of the XML file to be written.

nodePrefix

A character value giving the prefix to which the node index in 'mat' will be appended.

overwrite

If TRUE and file already exists, overwrite it.

...

Further arguments to be passed to plotKEGGgraph.

verbose

If TRUE, extra information is output.

Value

None.

See Also

parseKGML2Graph

Examples

library("KEGGgraph")
library("rrcov")

## Create a random graph
graph <- randomWAMGraph(nnodes=5, nedges=7, verbose=TRUE)
plot(graph)

## Retrieve its adjacency matrix
A <- graph@adjMat

## write it to KGML file
grPathname <- "randomWAMGraph.xml"
writeAdjacencyMatrix2KGML(A, pathname=grPathname, verbose=TRUE, overwrite=TRUE)

## read it from file
gr <- parseKGML2Graph(grPathname)

## Two examples of Laplacians from the same graph
lapMI <- laplacianFromA(A, ltype="meanInfluence")
print(lapMI)

lapN <- laplacianFromA(A, ltype="normalized")
print(lapN)

U <- lapN$U
p <- nrow(A)
sigma <- diag(p)/sqrt(p)

X <- twoSampleFromGraph(100, 120, shiftM2=1, sigma, U=U, k=3)

## T2
t <- T2.test(X$X1,X$X2)
str(t)

tu <- graph.T2.test(X$X1, X$X2, lfA=lapMI, k=3)
str(tu)