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aM2bpG<-function(aM){
if(is.null(rownames(aM))) stop("'aM' must have row names")
if(is.null(colnames(aM))) stop("'aM' must have column names")
V <- c(rownames(aM),colnames(aM))
tmat<-which(aM>0,arr.ind=TRUE)
tmat[,2] <- tmat[,2] + dim(aM)[1]
numN<-length(V)
numE<-dim(tmat)[1]
rval <- vector("list", length = numN)
for (i in seq_len(numE)) {
rval[[tmat[i, 1]]]$edges <- c(rval[[tmat[i, 1]]]$edges,
tmat[i, 2])
ln <- length(rval[[tmat[i, 1]]]$edges)
rval[[tmat[i, 1]]]$weights <- c(rval[[tmat[i, 1]]]$weights,
aM[tmat[i,1],(tmat[i,2]-dim(aM)[1])])
names(rval[[tmat[i, 1]]]$weights)[ln] <- tmat[i, 2]
}
names(rval) <- V
graphNEL(nodes = V, edgeL = rval, edgemode="directed")
}
## WH 23 June 2004, Ladir CH
ftM2adjM <- function(ft, W=NULL, V=NULL, edgemode="directed")
.ftM2other(ft, W, V, edgemode, "adjM")
ftM2graphNEL <- function(ft, W=NULL, V=NULL, edgemode="directed")
.ftM2other(ft, W, V, edgemode, "graphNEL")
.ftM2other <- function(ft, W, V, edgemode, targetclass) {
## ft: nx2 matrix.
if(!(is.matrix(ft) && ncol(ft)==2))
stop("'ft' must be an nx2 matrix")
numE <- nrow(ft)
## deal with W
if(is.null(W)) W <- rep(1,numE)
if(!length(W)==numE)
stop("length of 'W' must equal number of edges in 'ft'")
## deal with edgemode
if(!edgemode %in% c("undirected", "directed"))
stop("'edgemode' must be 'directed' or 'undirected'")
if(edgemode == "undirected") {
## reflect each pair -- but *not* the self-edges!
differ <- ft[,1] != ft[,2]
ft <- rbind(ft, ft[differ, 2:1])
W <- c( W, W[differ])
}
## deal with V
cft <- as.character(ft)
if(is.null(V))
V <- unique(cft)
ift <- array(match(cft, V), dim=dim(ft))
if(any(is.na(ift)))
stop("node names in 'ft' must be in 'V'")
numN <- length(V)
ind <- ift[,1]+(ift[,2]-1)*numN
if(any(duplicated(ind)))
stop("duplicate edges not allowed")
switch(targetclass,
adjM = {
mat <- matrix(0, ncol=numN, nrow=numN, dimnames=list(V,V))
mat[ind] <- W
mat
},
graphNEL = {
## ift[,2] are the indices of the to-nodes in V
## ft[,1] are the names of the from-nodes
## toN is a named list, whose names are the levels of ft[,1] and whose elements are the indices of to-nodes in V
## names(toN) is a subset of V, but not identical: the nodes with no outgoing edges are not in names(toN)
## Beware of partial matching! (This lead to a bug in earlier versions of this function, where edges were
## invented if there were nodes with no outgoing edges whose name partially matched the name of other
## nodes with outgoing edges.
toN <- split(ift[,2], ft[,1])
eW <- split(W, ft[,1])
edgeL <- lapply(V, function(x) list(edges=NULL, weights=NULL))
names(edgeL) <- V
mt = match(names(toN), V)
for(k in seq(along=mt))
edgeL[[mt[k]]] <- list(edges=toN[[k]], weights=eW[[k]])
graphNEL(nodes=V, edgeL=edgeL, edgemode=edgemode)
},
stop("'targetclass' unknown: ", sQuote(targetclass))
) ## end switch
}
setAs("matrix", "graphAM", function(from) {
if(!identical(ncol(from), nrow(from)))
stop("'ncol(from)' and 'nrow(from)' must be identical")
if(is.null(rownames(from))) {
rownames(from) = if(is.null(colnames(from))) {
paste(seq_len(nrow(from)))
} else {
colnames(from)
}
}
if(is.null(colnames(from))) {
colnames(from) = if(is.null(rownames(from))) {
paste(seq_len(ncol(from)))
} else {
rownames(from)
}
}
if(!identical(rownames(from),colnames(from)))
stop("'rownames(from)' and 'colnames(from)' must be identical")
if(!is.numeric(from))
storage.mode(from) = "integer"
emode <- if (all(from == t(from))) "undirected" else "directed"
defaultWeight <- vector(mode = typeof(from), length = 1L)
defaultWeight[1L] <- 1L
graphAM (from, edgemode=emode, values=list(weight=defaultWeight))
})
setAs("matrix", "graphNEL",
function(from) as(as(from, "graphAM"), "graphNEL"))
setAs("graphNEL", "matrix", function(from) {
as(as(from, "graphAM"), "matrix")
})
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