Nothing
ccgraph <-
function (x, main = NULL, seed = 0, maxiter = 100, alpha = c(1,
1, 1), scope, loops, collRecip, undRecip, showLbs, cex.main,
conc, coord, clu, cex, lwd, pch, lty, bwd, bwd2, att, bg,
mar, pos, asp, ecol, vcol, vcol0, lbs, col, lbat, swp, swp2,
scl, mirrorX, mirrorY, mirrorD, mirrorL, mirrorV, mirrorH,
rot, hds, vedist, ffamily, fstyle, fsize, fcol, nr, gens,
...)
{
pclu <- NULL
if (is.matrix(x) == TRUE && missing(gens) == TRUE)
stop("If matrix \"x\" is a semigroup, generators are not provided.")
ifelse(is.matrix(x) == TRUE && missing(gens) == FALSE, x <- multiplex::as.semigroup(x,
gens = gens), NA)
if (isTRUE(tolower(class(x)[1]) == "semigroup") == TRUE) {
ifelse(is.null(x$ord) == FALSE, n <- x$ord, n <- dim(x$S)[1])
if (all(x$st %in% dimnames(x$S)[[1]]) == TRUE) {
Lbs <- x$st
}
else {
Lbs <- dimnames(x$S)[[1]]
}
if (missing(gens) == FALSE) {
x$gens <- gens
}
else if (any(is.na(x$gens)) == TRUE || is.null(x$gens) ==
TRUE) {
message("Generators are not provided, and first element of 'x' is taken.")
x$gens <- 1
}
else {
NA
}
if (is.array(x$gens) == TRUE) {
cgm <- array(0, dim = c(n, n, dim(x$gens)[3]), dimnames = c(list(Lbs,
Lbs), list(attr(x$gens, "dimnames")[[3]])))
}
else if (is.vector(x$gens) == TRUE) {
if (identical(which(Lbs %in% x$gens), seq_len(length(x$gens))) ==
FALSE) {
pclu <- rep(1, n)
pclu[which(Lbs %in% x$gens)] <- 0
Sp <- as.data.frame(multiplex::perm(as.matrix(x$S),
clu = pclu))
cgm <- array(0, dim = c(n, n, length(x$gens)),
dimnames = c(dimnames(Sp), list(x$gens)))
}
else {
cgm <- array(0, dim = c(n, n, length(x$gens)),
dimnames = c(list(Lbs, Lbs), list(x$gens)))
}
}
else if (is.numeric(x$gens) == TRUE) {
cgm <- array(0, dim = c(n, n, x$gens), dimnames = c(list(Lbs,
Lbs), list(seq_len(x$gens))))
}
if (is.null(pclu) == TRUE) {
for (k in seq_len(dim(cgm)[3])) {
for (i in seq_len(n)) {
cgm[i, which(x$S[i, k] == Lbs), k] <- 1
}
rm(i)
}
rm(k)
}
else if (is.null(pclu) == FALSE) {
for (k in seq_len(dim(cgm)[3])) {
for (i in seq_len(n)) {
cgm[i, which(Sp[i, k] == colnames(Sp)), k] <- 1
}
rm(i)
}
rm(k)
}
}
else if (isTRUE(attr(x, "class") == "EdgeTable") == TRUE) {
if (is.null(x$ET) == FALSE) {
xet <- x$ET
}
else {
ifelse(is.list(x) == TRUE, xet <- x[[1]], stop("'x' must be a data frame in a list."))
}
ifelse(is.null(x$ord) == FALSE, n <- x$ord, n <- nrow(xet))
lb <- rownames(xet)
if (missing(gens) == TRUE) {
ifelse(is.null(x$gens) == FALSE, gens <- x$gens,
gens <- colnames(xet))
}
else {
invisible(NA)
}
ifelse(identical(as.numeric(gens), as.numeric(colnames(xet))) ==
TRUE, cgm <- array(0, dim = c(n, n, length(gens)),
dimnames = list(lb, lb, gens)), cgm <- array(0, dim = c(n,
n, dim(gens)[3]), dimnames = list(lb, lb, attr(gens,
"dimnames")[[3]])))
for (k in seq_len(dim(cgm)[3])) {
for (i in seq_len(n)) {
cgm[i, which(xet[i, k] == lb), k] <- 1
}
rm(i)
}
rm(k)
}
else {
if (is.array(x) == FALSE)
stop("Data must be at least a stacked array of square matrices.")
x <- multiplex::semigroup(x, type = "symbolic")
cgm <- array(0, dim = c(x$ord, x$ord, dim(x$gens)[3]),
dimnames = c(list(x$st, x$st), list(attr(x$gens,
"dimnames")[[3]])))
for (k in seq_len(dim(cgm)[3])) {
for (i in seq_len(x$ord)) {
cgm[i, which(x$S[i, k] == x$st), k] <- 1
}
rm(i)
}
rm(k)
}
net <- cgm
ifelse(is.null(pclu) == TRUE, NA, net <- multiplex::perm(net,
clu = c(which(pclu == 0), which(pclu == 1))))
ifelse(isTRUE(dim(net)[3] == 1) == TRUE, net <- net[, , 1],
NA)
if (isTRUE(n == 1L) == TRUE)
stop("1-element semigroup detected, and not yet supported")
ifelse(missing(undRecip) == FALSE && isTRUE(undRecip == TRUE) ==
TRUE, undRecip <- TRUE, undRecip <- FALSE)
ifelse(missing(loops) == FALSE && isTRUE(loops == FALSE) ==
TRUE, loops <- FALSE, loops <- TRUE)
ifelse(missing(collRecip) == FALSE && isTRUE(collRecip ==
FALSE) == TRUE, collRecip <- FALSE, collRecip <- TRUE)
ifelse(missing(conc) == FALSE && isTRUE(conc == TRUE) ==
TRUE, conc <- TRUE, conc <- FALSE)
ifelse(missing(mirrorH) == FALSE && isTRUE(mirrorH == TRUE) ==
TRUE, mirrorY <- TRUE, NA)
ifelse(missing(mirrorV) == FALSE && isTRUE(mirrorV == TRUE) ==
TRUE, mirrorX <- TRUE, NA)
if (missing(showLbs) == FALSE && isTRUE(showLbs == TRUE) ==
TRUE) {
showLbs <- TRUE
}
else if (missing(showLbs) == FALSE && isTRUE(showLbs == FALSE) ==
TRUE) {
showLbs <- FALSE
}
else {
ifelse(is.null(dimnames(net)[[1]]) == FALSE, showLbs <- TRUE,
showLbs <- FALSE)
}
ifelse(missing(swp) == FALSE && isTRUE(swp == TRUE) == TRUE,
swp <- TRUE, swp <- FALSE)
ifelse(missing(swp2) == FALSE && isTRUE(swp2 == TRUE) ==
TRUE, swp2 <- TRUE, swp2 <- FALSE)
if (missing(scope) == FALSE) {
if (isTRUE(is.list(scope) == TRUE) == FALSE)
stop("\"scope\" should be a list or a vector of lists.")
scope <- list(scope)
ifelse(is.null(scope[[1]]) == TRUE, scope <- scope[2:length(scope)],
NA)
if (isTRUE(length(scope) > 1L) == TRUE && isTRUE(names(scope[1]) ==
"coord") == TRUE) {
scope <- scope[rev(seq_len(length(scope)))]
flgrev <- TRUE
}
else {
flgrev <- FALSE
}
tmp <- scope[[1]]
if (isTRUE(length(scope) > 1L) == TRUE && isTRUE(length(scope[[1]]) >
1L) == TRUE) {
for (k in 2:length(scope)) {
tmp[length(tmp) + 1L] <- as.list(scope[k])
names(tmp)[length(tmp)] <- attr(scope[k], "names")
}
rm(k)
}
else if (isTRUE(length(scope) > 1L) == TRUE) {
names(tmp) <- attr(scope[1], "names")
for (k in 2:length(scope)) {
if (is.list(scope[[k]]) == TRUE && is.data.frame(scope[[k]]) ==
FALSE) {
for (j in seq_len(length(scope[[k]]))) {
tmp[length(tmp) + 1L] <- as.list(scope[[k]][j])
names(tmp)[length(tmp)] <- attr(scope[[k]][j],
"names")
}
rm(j)
}
else if (is.data.frame(scope[[k]]) == FALSE) {
tmp[length(tmp) + 1L] <- as.list(scope[k])
names(tmp)[length(tmp)] <- attr(scope[k], "names")
}
else if (is.data.frame(scope[[k]]) == TRUE) {
tmp[length(tmp) + 1L] <- as.vector(scope[k])
names(tmp)[length(tmp)] <- attr(scope[k], "names")
}
else {
NA
}
}
rm(k)
}
else {
tmp <- scope[[1]]
}
ifelse(isTRUE(flgrev == TRUE) == TRUE, scope <- tmp[rev(seq_len(length(tmp)))],
scope <- tmp)
for (i in seq_len(length(scope))) {
if (isTRUE(names(scope)[i] %in% c("seed", "main")) ==
TRUE) {
tmpi <- as.vector(scope[[i]])
assign(names(scope)[i], get("tmpi"))
}
else {
if (is.null((scope[[i]])) == FALSE) {
tmpi <- as.vector(scope[[i]])
ifelse(isTRUE(names(scope)[i] != "") == TRUE,
assign(names(scope)[i], get("tmpi")), NA)
}
}
}
rm(i)
}
else {
NA
}
ifelse(missing(asp) == TRUE, asp <- 1, NA)
ifelse(missing(lwd) == TRUE, lwd <- 1, NA)
ifelse(missing(pch) == TRUE, pch <- 21, NA)
ifelse(missing(fcol) == TRUE, fcol <- 1, NA)
ifelse(missing(bwd) == TRUE, bwd <- 1, NA)
ifelse(isTRUE(bwd < 0L) == TRUE, bwd <- 0L, NA)
ifelse(missing(bg) == TRUE, bg <- graphics::par()$bg, NA)
ifelse(missing(cex.main) == TRUE, cex.main <- graphics::par()$cex.main,
NA)
ifelse(missing(rot) == TRUE, NA, rot <- rot[1] * -1)
if (isTRUE(length(alpha) < 2) == TRUE) {
alfa <- 1
alpha <- rep(alpha, 3)
}
else {
alfa <- alpha[2]
}
if (isTRUE(length(alpha) < 3) == TRUE)
alpha <- append(alpha, 0.1)
if (!(missing(hds)) && missing(scl) == TRUE) {
if (isTRUE(hds > 1L) == TRUE) {
hds <- (hds/1.5)
}
else if (isTRUE(hds < 1L) == TRUE) {
hds <- (hds/(hds + 0.15))
}
else if (isTRUE(hds == 0L) == TRUE) {
hds <- 0.01
}
else {
NA
}
}
else {
ifelse(missing(scl) == TRUE, hds <- 1L, hds <- 1L * scl)
}
ifelse(isTRUE(dim(net)[1] > 8) == TRUE || isTRUE(lwd >= 3) ==
TRUE, hds <- hds * 0.75, NA)
ifelse(missing(scl) == TRUE, scl <- rep(1, 2), NA)
ifelse(isTRUE(length(scl) == 1) == TRUE, scl <- rep(scl,
2), scl <- scl[1:2])
ifelse(missing(vedist) == TRUE, vedist <- 0, NA)
if (isTRUE(vedist > 10L) == TRUE) {
vedist <- 10L
}
else if (isTRUE(vedist < (-10L)) == TRUE) {
vedist <- -10L
}
if (missing(lbs) == TRUE) {
ifelse(is.null(dimnames(net)[[1]]) == TRUE, lbs <- as.character(seq_len(dim(net)[1])),
lbs <- dimnames(net)[[1]])
}
else {
NA
}
n <- dim(net)[1]
ifelse(isTRUE(is.na(dim(net)[3]) == TRUE) == TRUE, z <- 1L,
z <- dim(net)[3])
ifelse(isTRUE(swp == TRUE) == TRUE && isTRUE(z > 1L) == TRUE,
net <- net[, , rev(seq_len(z))], NA)
netd <- multiplex::dichot(net, c = 1L)
if (isTRUE(collRecip == TRUE) == TRUE) {
if (isTRUE(z == 1L) == TRUE) {
nt <- netd + t(netd)
rcp <- multiplex::dichot(nt, c = 2L)
rcp[lower.tri(rcp, diag = TRUE)] <- 0L
}
else {
nt <- array(0L, dim = c(n, n, z))
dimnames(nt)[[1]] <- dimnames(nt)[[2]] <- lbs
dimnames(nt)[[3]] <- dimnames(net)[[3]]
for (i in seq_len(z)) {
nt[, , i] <- netd[, , i] + t(netd[, , i])
}
rm(i)
rcp <- multiplex::dichot(nt, c = 2L)
for (i in seq_len(z)) {
rcp[, , i][lower.tri(rcp[, , i], diag = TRUE)] <- 0L
}
rm(i)
}
ucnet <- netd - rcp
}
else {
ucnet <- netd
}
bd <- multiplex::bundles(netd, loops = loops, lb2lb = FALSE,
collapse = FALSE)
ifelse(isTRUE(z == 1L) == TRUE, r <- 1L, r <- length(bd[[1]]))
ifelse(isTRUE(sum(net) == 0) == TRUE && isTRUE(loops == TRUE) ==
TRUE, bd$loop <- character(0), NA)
bds <- multiplex::summaryBundles(bd, byties = TRUE)
ifelse(missing(ecol) == TRUE, ecol <- grDevices::gray.colors(r,
start = 0.1, end = 0.5), NA)
ifelse(missing(lty) == TRUE, lty <- seq_len(r), NA)
if (isTRUE(z == 1L) == TRUE) {
Lt <- lty[1]
vecol <- ecol[1]
}
else {
ifelse(isTRUE(length(ecol) == 1L) == TRUE, vecol <- rep(ecol,
z), vecol <- rep(ecol, z)[seq_len(z)])
ifelse(isTRUE(length(lty) == 1L) == TRUE, Lt <- seq_len(r),
Lt <- rep(lty, r)[seq_len(r)])
if (isTRUE(length(lty) == length(Lt)) == FALSE) {
Ltc <- seq_along(vecol)
}
else {
if (isTRUE(seq(lty) == lty) == TRUE) {
Ltc <- Lt
}
else {
ifelse(isTRUE(swp == TRUE) == TRUE, Ltc <- rev(seq_len(r)),
Ltc <- seq_len(r))
}
}
}
vltz <- Lt
if (missing(clu) == FALSE) {
if (is.vector(as.vector(clu)) == FALSE)
stop("'clu' must be a vector")
if (is.factor(clu) == TRUE) {
tmpclu <- clu
for (i in seq_len(nlevels(factor(clu)))) {
levels(clu) <- c(levels(clu), i)
clu[which(levels(factor(tmpclu))[i] == clu)] <- i
}
rm(i)
clu <- methods::as(as.vector(clu), "numeric")
rm(tmpclu)
}
else if (is.character(clu) == TRUE) {
tmpclu <- clu
clu[which(clu == clu[1])] <- 1
for (i in seq_len(nlevels(factor(tmpclu)) - 1L)) {
clu[which(clu == clu[which((clu %in% tmpclu) ==
TRUE)[(i - 0)]])] <- (i + 1L)
}
rm(i)
clu[which((clu %in% tmpclu) == TRUE)] <- nlevels(factor(tmpclu))
clu <- methods::as(as.vector(clu), "numeric")
rm(tmpclu)
}
else {
NA
}
clu[which(is.na(clu))] <- 0
nclu <- nlevels(factor(clu))
}
else {
nclu <- 1L
}
flgcx <- FALSE
if (missing(cex) == TRUE && isTRUE(loops == FALSE) == TRUE) {
if (isTRUE(length(bds) == 0) == TRUE) {
cex <- 1L
}
else {
cex <- length(bds[[1]])/2L
if (isTRUE(length(bds) > 1L) == TRUE) {
for (i in 2:length(bds)) ifelse(isTRUE(cex <
(length(bds[[i]])/2L)) == TRUE, cex <- (length(bds[[i]])/2L),
NA)
}
cex <- ceiling(cex)
}
}
else if (missing(cex) == TRUE) {
cex <- 1L
}
if (isTRUE(length(cex) == 1L) == TRUE) {
cex <- rep(cex, n)
}
else {
if (is.vector(cex) == FALSE)
stop("'cex' must be a vector")
cex[which(is.na(cex))] <- 0
cex <- cex[seq_len(n)]
flgcx <- TRUE
}
if (isTRUE(flgcx == TRUE) == TRUE && isTRUE(max(cex) > 10L) ==
TRUE) {
if (isTRUE(mean(cex) > 20L) == TRUE) {
cex <- (((cex - min(cex))/(max(cex) - min(cex))) *
10L)
}
else {
cex <- (cex/(norm(as.matrix(cex), type = "M"))) *
10L
}
ifelse(isTRUE(min(cex) == 0) == TRUE, cex <- cex + 1L +
(2L/n), NA)
}
else if (isTRUE(flgcx == FALSE) == TRUE) {
ifelse(isTRUE(max(cex) >= 21L) == TRUE, cex <- 20L, NA)
}
else {
NA
}
if (missing(fsize) == TRUE) {
ifelse(isTRUE(max(cex) < 2) == TRUE, fsize <- cex * 0.66,
fsize <- cex * 0.33)
}
else {
fsize <- fsize/10
}
ifelse(isTRUE(bwd > 1L) == TRUE, bwd <- 1L, NA)
ifelse(isTRUE(max(cex) < 2) == TRUE, NA, bwd <- bwd * 0.75)
if (isTRUE(length(pch) == 1L) == TRUE) {
pch <- rep(pch, n)
}
else if (isTRUE(length(pch) == nclu) == TRUE) {
if (identical(pch, clu) == FALSE) {
tmppch <- rep(0, n)
for (i in seq_len(nclu)) {
tmppch[which(clu == (levels(factor(clu))[i]))] <- pch[i]
}
rm(i)
pch <- tmppch
rm(tmppch)
}
}
else if (isTRUE(length(pch) != n) == TRUE) {
pch <- rep(pch[1], n)
}
if (missing(vcol) == TRUE) {
vcol <- grDevices::gray.colors(nclu)
ifelse(missing(col) == TRUE, NA, vcol <- col)
}
else {
if (isTRUE(length(vcol) == 1L) == TRUE) {
vcol <- rep(vcol, n)
}
else if (isTRUE(length(vcol) == nclu) == TRUE) {
if (identical(vcol, clu) == FALSE) {
tmpvcol <- rep(0, n)
for (i in seq_len(nclu)) {
tmpvcol[which(clu == (levels(factor(clu))[i]))] <- vcol[i]
}
rm(i)
vcol <- tmpvcol
rm(tmpvcol)
}
}
else if (isTRUE(length(vcol) != n) == TRUE & isTRUE(nclu ==
1) == TRUE) {
vcol <- rep(vcol[1], n)
}
vcol[which(is.na(vcol))] <- graphics::par()$bg
vcol[which(vcol == 0)] <- graphics::par()$bg
}
if (isTRUE(any(pch %in% 21:25)) == TRUE) {
if (missing(vcol0) == TRUE) {
vcol0 <- vcol
}
else {
ifelse(missing(vcol0) == TRUE, NA, vcol0[which(is.na(vcol0))] <- 1)
}
if (isTRUE(length(vcol0) == 1L) == TRUE) {
vcol0 <- rep(vcol0, n)
}
else if (isTRUE(length(vcol0) == nclu) == TRUE) {
if (identical(vcol0, clu) == FALSE) {
tmpvcol0 <- rep(0, n)
for (i in seq_len(nclu)) {
tmpvcol0[which(clu == (levels(factor(clu))[i]))] <- vcol0[i]
}
rm(i)
vcol0 <- tmpvcol0
rm(tmpvcol0)
}
}
else if (isTRUE(length(vcol0) != n) == TRUE | isTRUE(nclu ==
1) == TRUE) {
vcol0 <- rep(vcol0[1], n)
}
}
else {
vcol0 <- vcol
}
ifelse(isTRUE(n > 20) == TRUE, ffds <- 0.2, ffds <- 0)
fds <- 130L - (n * ffds)
if (isTRUE(flgcx == TRUE) == TRUE) {
fds <- fds - 10L
}
else if (isTRUE(flgcx == FALSE) == TRUE) {
NA
}
if (isTRUE(max(scl) < 1) == TRUE) {
fds <- fds - (1/(mean(scl)/30L))
}
else if (isTRUE(max(scl) > 1) == TRUE) {
fds <- fds + (mean(scl) * 20L)
}
else {
NA
}
if (missing(coord) == FALSE) {
if (isTRUE(nrow(coord) == n) == FALSE)
stop("Length of 'coord' does not match network order.")
flgcrd <- TRUE
crd <- coord
}
else if (missing(coord) == TRUE) {
flgcrd <- FALSE
ifelse(isTRUE(conc == TRUE) == FALSE, crd <- frcd(netd,
seed = seed, maxiter = maxiter), crd <- conc(netd,
nr, ...))
}
if (missing(rot) == FALSE) {
crd[, 1:2] <- xyrt(crd[, 1:2], as.numeric(rot))
crd[, 1:2] <- crd[, 1:2] - min(crd[, 1:2])
cnt <- 1L
ifelse(isTRUE(n == 2) == TRUE && isTRUE(rot == -90) ==
TRUE, rot <- -89.9, NA)
}
else {
cnt <- 0
}
if (missing(pos) == TRUE) {
pos <- 4
}
else {
if (isTRUE(pos < 0L) == TRUE | isTRUE(pos > 4L) == TRUE)
stop("Invalid \"pos\" value.")
}
ifelse(missing(mirrorX) == FALSE && isTRUE(mirrorX == TRUE) ==
TRUE, crd[, 1] <- crd[, 1] * cos(pi) - crd[, 2] * sin(pi),
mirrorX <- FALSE)
ifelse(missing(mirrorY) == FALSE && isTRUE(mirrorY == TRUE) ==
TRUE, crd[, 2] <- crd[, 2] * cos(pi) - crd[, 1] * sin(pi),
mirrorY <- FALSE)
if (missing(mirrorL) == FALSE && isTRUE(mirrorL == TRUE) ==
TRUE) {
crd[, 1:2] <- xyrt(crd[, 1:2], as.numeric(45))
crd[, 1:2] <- crd[, 1:2] - min(crd[, 1:2])
crd[, 2] <- crd[, 2] * cos(pi) - crd[, 1] * sin(pi)
crd[, 1:2] <- xyrt(crd[, 1:2], as.numeric(-45))
crd[, 1:2] <- crd[, 1:2] - min(crd[, 1:2])
}
else if (missing(mirrorD) == FALSE && isTRUE(mirrorD == TRUE) ==
TRUE) {
crd[, 1:2] <- xyrt(crd[, 1:2], as.numeric(-45))
crd[, 1:2] <- crd[, 1:2] - min(crd[, 1:2])
crd[, 2] <- crd[, 2] * cos(pi) - crd[, 1] * sin(pi)
crd[, 1:2] <- xyrt(crd[, 1:2], as.numeric(45))
crd[, 1:2] <- crd[, 1:2] - min(crd[, 1:2])
}
else {
NA
}
if (isTRUE(n > 1) == TRUE) {
rat <- (max(crd[, 1]) - min(crd[, 1]))/(max(crd[, 2]) -
min(crd[, 2]))
crd[, 1] <- (crd[, 1] - min(crd[, 1]))/(max(crd[, 1]) -
min(crd[, 1]))
ifelse(isTRUE(rat > 0) == TRUE, crd[, 2] <- ((crd[, 2] -
min(crd[, 2]))/(max(crd[, 2]) - min(crd[, 2]))) *
(1L/rat), crd[, 2] <- ((crd[, 2] - min(crd[, 2]))/(max(crd[,
2]) - min(crd[, 2]))) * (rat))
}
else {
NA
}
fds <- fds + (vedist * -10)
if (isTRUE(flgcrd == TRUE) == TRUE && isTRUE(ncol(crd) >
2) == TRUE) {
lbgml <- tolower(as.vector(crd[, 3]))
lbnet <- tolower(as.vector(lbs))
lbp <- vector()
for (i in seq_len(nrow(crd))) {
lbp <- append(lbp, which(lbnet[i] == lbgml))
}
rm(i)
if (isTRUE(ncol(crd) > 3) == TRUE) {
atgml <- as.vector(crd[, 4])
atgml[which(is.na(atgml))] <- ""
atts <- atgml[lbp]
}
nds <- data.frame(X = as.numeric(as.vector(crd[lbp, 1])),
Y = as.numeric(as.vector(crd[lbp, 2])))
}
else {
nds <- data.frame(X = as.numeric(as.vector(crd[, 1])),
Y = as.numeric(as.vector(crd[, 2])))
}
nds <- ((2L/max(nds * (0.75))) * (nds * 0.75)) * (0.5)
mscl <- mean(scl)
cex <- cex * mscl
fsize <- fsize * mscl
omr <- graphics::par()$mar
omi <- graphics::par()$mai
if (missing(mar) == TRUE) {
mar <- c(0, 0, 0, 0)
}
else {
mar <- omr
}
ifelse(is.null(main) == TRUE, graphics::par(mar = mar), graphics::par(mar = mar +
c(0, 0, cex.main, 0)))
obg <- graphics::par()$bg
graphics::par(bg = grDevices::adjustcolor(bg, alpha = alpha[3]))
if (isTRUE(loops == TRUE) == TRUE) {
ylim <- c(min(nds[, 2]) - (max(cex)/100L), max(nds[,
2]) + (max(cex)/70L))
xlim <- c(min(nds[, 1]) - (max(cex)/100L), max(nds[,
1]) + (max(cex)/100L))
}
else if (isTRUE(flgcx == TRUE) == TRUE) {
ylim <- c(min(nds[, 2]) - (max(cex)/500L), max(nds[,
2]) + (max(cex)/500L))
xlim <- c(min(nds[, 1]) - (max(cex)/500L), max(nds[,
1]) + (max(cex)/500L))
}
else {
ylim <- c(min(nds[, 2]) - ((cex[1])/200L), max(nds[,
2]) + ((cex[1])/200L))
xlim <- c(min(nds[, 1]) - ((cex[1])/200L), max(nds[,
1]) + ((cex[1])/200L))
}
suppressWarnings(graphics::plot(nds, type = "n", axes = FALSE,
xlab = "", ylab = "", ylim = ylim, xlim = xlim, asp = asp,
main = main, cex.main = cex.main, ...))
tlbs <- vector()
if (isTRUE(length(bds) > 0) == TRUE) {
for (i in seq_len(length(attr(bds, "names")))) {
ifelse(isTRUE(length(multiplex::dhc(attr(bds, "names")[i],
sep = "")) > 4L) == TRUE, tlbs <- append(tlbs,
tolower(paste(multiplex::dhc(attr(bds, "names")[i],
sep = "")[1:4], collapse = ""))), tlbs <- append(tlbs,
tolower(attr(bds, "names"))[i]))
}
rm(i)
}
if (isTRUE(loops == TRUE) == TRUE) {
tlbslp <- tlbs
tlbs <- tlbs[which(tlbs != "loop")]
}
else {
NA
}
if (isTRUE(swp == TRUE) == TRUE) {
Lt <- Lt[rev(seq_len(length(Lt)))]
lwd <- lwd[length(lwd):1]
alfa <- alfa[rev(seq_len(length(alfa)))]
}
if (isTRUE(collRecip == TRUE) == TRUE) {
trcp <- multiplex::transf(rcp, type = "tolist")
}
else {
NA
}
if (isTRUE(length(tlbs) > 0) == TRUE) {
for (k in seq_len(length(tlbs))) {
prs <- as.numeric(multiplex::dhc(bds[[k]]))
pars <- as.matrix(nds[as.numeric(levels(factor(multiplex::dhc(bds[[k]])))),
])
rbds <- length(bds[[k]])
if (isTRUE(rbds > 0L) == TRUE) {
q <- which(tlbs[k] == attr(bd, "names"))
if (isTRUE(z == 1L) == TRUE) {
vlt <- rep(Lt, rbds)
vecol <- rep(ecol[1], rbds)
tbnd <- as.vector(unlist(bd[q]))
if (isTRUE(length(tbnd) > 0L) == TRUE) {
ifelse(isTRUE(any(tbnd %in% bds[[k]])) ==
TRUE, vlt <- append(vlt, rep(Lt, q)), NA)
ifelse(isTRUE(any(tbnd %in% bds[[k]])) ==
TRUE, vltz <- append(vltz, rep(Lt, q)),
NA)
}
vltc <- vlt[1]
}
else {
vlt <- vector()
for (i in seq_along(Lt)) {
tbnd <- as.vector(unlist(bd[[q]][i]))
if (isTRUE(length(tbnd) > 0L) == TRUE) {
ifelse(isTRUE(any(tbnd %in% bds[[k]])) ==
TRUE, vlt <- append(vlt, rep(Lt[i], length(which(tbnd %in%
bds[[k]])))), NA)
ifelse(isTRUE(any(tbnd %in% bds[[k]])) ==
TRUE, vltz <- append(vltz, rep(Lt[i],
length(which(tbnd %in% bds[[k]])))),
NA)
}
}
rm(i)
if (isTRUE(length(lty) == 1L) == TRUE) {
vlt1 <- rep(lty, length(vlt))
vltc <- vlt
}
else {
vltc <- vector()
if (isTRUE(Lt == Ltc) == FALSE) {
for (i in seq_along(Ltc)) {
tbnd <- as.vector(unlist(bd[[q]][i]))
if (isTRUE(length(tbnd) > 0L) == TRUE) {
ifelse(isTRUE(any(tbnd %in% bds[[k]])) ==
TRUE, vltc <- append(vltc, rep(Ltc[i],
length(which(tbnd %in% bds[[k]])))),
NA)
}
}
rm(i)
}
else {
if (isTRUE(seq(lty) == lty) == TRUE) {
vltc <- vlt
}
else {
for (i in seq_along(lty)) {
vltc <- append(vltc, replace(vlt[which(vlt ==
lty[i])], vlt[which(vlt == lty[i])] !=
i, i))
}
rm(i)
}
}
}
}
cx <- cex
lw <- rep(lwd[1], rbds)
ifelse(isTRUE(swp2 == TRUE) == TRUE && isTRUE(tlbs[k] %in%
c("recp")) == TRUE, bds[[k]] <- multiplex::swp(bds[[k]]),
NA)
if (isTRUE(collRecip == TRUE) == TRUE && isTRUE(tlbs[k] %in%
c("recp")) == TRUE) {
bw <- 0L
ifelse(isTRUE(undRecip == TRUE) == TRUE, hd <- 0L,
hd <- hds)
lw <- (lw + (3L/lw)) * mscl
}
else if (isTRUE(collRecip == TRUE) == FALSE &&
isTRUE(tlbs[k] %in% c("recp")) == TRUE) {
ifelse(isTRUE(undRecip == TRUE) == TRUE, hd <- 0L,
hd <- hds)
}
else {
bw <- bwd
hd <- hds
lw <- lw * mscl
}
if (isTRUE(collRecip == TRUE) == TRUE && isTRUE(tlbs[k] %in%
c("recp")) == FALSE) {
flgcr <- numeric()
sbds <- multiplex::swp(bds[[k]])
if (any(sbds %in% unlist(trcp)) == TRUE) {
for (i in seq_len(z)) {
ifelse(any(sbds %in% trcp[[i]]) == TRUE,
flgcr <- append(flgcr, as.numeric(i)),
NA)
}
rm(i)
}
}
else {
flgcr <- rep(0L, z)
}
pars[, 1] <- pars[, 1] * scl[1]
pars[, 2] <- pars[, 2] * scl[2]
if (isTRUE(z == 1L) == TRUE) {
ccbnd(pars, rbds, bds[[k]], vlt, cx * mscl,
lw, vecol, bw, alfa, fds, flgcx, flgcr, hd,
n)
}
else {
ifelse(isTRUE(length(lty) == 1L) == TRUE, ccbnd(pars,
rbds, bds[[k]], vlt1, cx * mscl, lw, vecol[vltc],
bw, alfa, fds, flgcx, flgcr, hd, n), ccbnd(pars,
rbds, bds[[k]], vlt, cx * mscl, lw, vecol[vltc],
bw, alfa, fds, flgcx, flgcr, hd, n))
}
}
else {
NA
}
}
rm(k)
}
else {
NA
}
if (isTRUE(loops == TRUE) == TRUE) {
ifelse(isTRUE(swp == TRUE) == TRUE && isTRUE(z == 2L) ==
TRUE, Lt <- rev(Lt), NA)
bdlp <- bd$loop
ndss <- nds
ndss[, 1] <- ndss[, 1] * scl[1]
ndss[, 2] <- ndss[, 2] * scl[2]
dz <- (rng(z) + abs(min(rng(z))))/(10L)
if (isTRUE(z == 1L) == TRUE) {
lp <- as.vector(which(diag(net) > 0))
if (isTRUE(length(lp) > 0) == TRUE) {
for (i in seq_len(length(lp))) {
if (isTRUE(n < 3) == TRUE) {
dcx <- (cex[lp[i]] * 0.0075)
lpsz <- (cex[lp[i]] * 0.005) - (dz)
}
else {
dcx <- (cex[lp[i]] * 0.01)
lpsz <- (cex[lp[i]] * 0.0075) - (dz)
}
hc(ndss[lp[i], 1], ndss[lp[i], 2] + (dcx),
lpsz, col = vecol, lty = Lt, lwd = lwd)
}
rm(i)
}
else {
NA
}
}
else if (isTRUE(z > 1) == TRUE) {
if (missing(bwd2) == TRUE) {
NA
}
else {
ifelse(isTRUE(bwd2 < 1L) == TRUE && isTRUE(bwd2 ==
0) == FALSE, bwd2 <- 1L, NA)
ifelse(isTRUE(bwd2 > 2L) == TRUE, bwd2 <- 2L,
NA)
if (isTRUE(bwd2 == 0) == TRUE || (any(duplicated(unlist(bdlp))) ==
FALSE && isTRUE(bwd2 == 1L) == TRUE)) {
dz <- rep(0, z)
}
else {
ifelse(missing(bwd2) == TRUE, dz <- (rng(z) +
abs(min(rng(z))))/(10L), dz <- (bwd2) * (rng(z) +
abs(min(rng(z))))/(4))
}
}
ifelse(isTRUE(cx > 3L) == TRUE, fcex <- 3L, fcex <- floor(cx))
for (k in seq_len(length(bdlp))) {
lp <- as.numeric(unique(multiplex::dhc(bdlp)[k][[1]]))
if (isTRUE(length(lp) > 0) == TRUE) {
for (i in seq_len(length(lp))) {
ifelse(isTRUE(fcex[lp[i]] <= 3L) == TRUE |
isTRUE(n < 3L) == TRUE, dz <- dz * 0.75,
NA)
if (isTRUE(n < 3L) == TRUE) {
dcx <- fcex[lp[i]]/110L
lpsz <- abs((fcex[lp[i]] * 0.007) - dz[k])
}
else {
dcx <- fcex[lp[i]]/100L
lpsz <- abs((fcex[lp[i]] * 0.0075) - dz[k])
}
ifelse(isTRUE(length(lty) == 1) == TRUE,
hc(ndss[lp[i], 1], ndss[lp[i], 2] + (dcx),
lpsz, col = grDevices::adjustcolor(vecol[k],
alpha = alfa), lty = lty, lwd = lwd[k]),
hc(ndss[lp[i], 1], ndss[lp[i], 2] + (dcx),
lpsz, col = grDevices::adjustcolor(vecol[k],
alpha = alfa), lty = Lt[k], lwd = lwd[k]))
}
rm(i)
}
else {
dz <- append(0, dz)
}
}
rm(k)
}
}
else {
NA
}
if (all(pch %in% 21:25) == TRUE) {
graphics::points(nds[, 1] * scl[1], nds[, 2] * scl[2],
pch = pch, cex = cex, col = grDevices::adjustcolor(vcol0,
alpha = alpha[1]), bg = grDevices::adjustcolor(vcol,
alpha = alpha[1]))
}
else {
graphics::points(nds[, 1] * scl[1], nds[, 2] * scl[2],
pch = pch, cex = cex, col = grDevices::adjustcolor(vcol,
alpha = alpha[1]), bg = grDevices::adjustcolor(vcol,
alpha = alpha[1]))
}
if (isTRUE(showLbs == TRUE) == TRUE) {
ndss <- nds
ndss[, 1] <- ndss[, 1] * scl[1]
ndss[, 2] <- ndss[, 2] * scl[2]
ifelse(missing(ffamily) == FALSE && isTRUE(ffamily %in%
names(grDevices::postscriptFonts())) == TRUE, graphics::par(family = ffamily),
NA)
if (isTRUE(length(pos) == 1) == TRUE) {
if (isTRUE(pos == 0) == TRUE) {
if (missing(fstyle) == TRUE || (missing(fstyle) ==
FALSE && isTRUE(fstyle %in% c("italic", "bold",
"bolditalic") == FALSE))) {
graphics::text(ndss, labels = lbs, cex = fsize,
adj = 0.5, col = fcol)
}
else if (missing(fstyle) == FALSE) {
if (isTRUE(fstyle == "italic") == TRUE) {
graphics::text(ndss, labels = as.expression(lapply(lbs,
function(x) bquote(italic(.(x))))), cex = fsize,
adj = 0.5, col = fcol)
}
else if (isTRUE(fstyle == "bold") == TRUE) {
graphics::text(ndss, labels = as.expression(lapply(lbs,
function(x) bquote(bold(.(x))))), cex = fsize,
adj = 0.5, col = fcol)
}
else if (isTRUE(fstyle == "bolditalic") ==
TRUE) {
graphics::text(ndss, labels = as.expression(lapply(lbs,
function(x) bquote(bolditalic(.(x))))),
cex = fsize, adj = 0.5, col = fcol)
}
}
}
else {
if (missing(fstyle) == TRUE || (missing(fstyle) ==
FALSE && isTRUE(fstyle %in% c("italic", "bold",
"bolditalic") == FALSE))) {
graphics::text(ndss, lbs, cex = fsize, pos = pos,
col = fcol, offset = (cex/4L), adj = c(0.5,
1))
}
else if (missing(fstyle) == FALSE) {
if (isTRUE(fstyle == "italic") == TRUE) {
graphics::text(ndss, as.expression(lapply(lbs,
function(x) bquote(italic(.(x))))), cex = fsize,
pos = pos, col = fcol, offset = (cex/4L),
adj = c(0.5, 1))
}
else if (isTRUE(fstyle == "bold") == TRUE) {
graphics::text(ndss, as.expression(lapply(lbs,
function(x) bquote(bold(.(x))))), cex = fsize,
pos = pos, col = fcol, offset = (cex/4L),
adj = c(0.5, 1))
}
else if (isTRUE(fstyle == "bolditalic") ==
TRUE) {
graphics::text(ndss, as.expression(lapply(lbs,
function(x) bquote(bolditalic(.(x))))),
cex = fsize, pos = pos, col = fcol, offset = (cex/4L),
adj = c(0.5, 1))
}
}
}
}
else if (isTRUE(length(pos) == n) == TRUE) {
if (missing(fstyle) == TRUE || (missing(fstyle) ==
FALSE && isTRUE(fstyle %in% c("italic", "bold",
"bolditalic") == FALSE))) {
graphics::text(ndss, lbs, cex = fsize, pos = pos,
col = fcol[1], offset = (cex/4L), adj = c(0.5,
1))
}
else if (missing(fstyle) == FALSE) {
if (isTRUE(fstyle == "italic") == TRUE) {
graphics::text(ndss, as.expression(lapply(lbs,
function(x) bquote(italic(.(x))))), cex = fsize,
pos = pos, col = fcol[1], offset = (cex/4L),
adj = c(0.5, 1))
}
else if (isTRUE(fstyle == "bold") == TRUE) {
graphics::text(ndss, as.expression(lapply(lbs,
function(x) bquote(bold(.(x))))), cex = fsize,
pos = pos, col = fcol[1], offset = (cex/4L),
adj = c(0.5, 1))
}
else if (isTRUE(fstyle == "bolditalic") == TRUE) {
graphics::text(ndss, as.expression(lapply(lbs,
function(x) bquote(bolditalic(.(x))))), cex = fsize,
pos = pos, col = fcol[1], offset = (cex/4L),
adj = c(0.5, 1))
}
}
}
else {
if (isTRUE(pos[1] == 0) == TRUE) {
if (missing(fstyle) == TRUE || (missing(fstyle) ==
FALSE && isTRUE(fstyle %in% c("italic", "bold",
"bolditalic") == FALSE))) {
graphics::text(ndss, labels = lbs, cex = fsize,
adj = 0.5, col = fcol)
}
else if (missing(fstyle) == FALSE) {
if (isTRUE(fstyle == "italic") == TRUE) {
graphics::text(ndss, labels = as.expression(lapply(lbs,
function(x) bquote(italic(.(x))))), cex = fsize,
adj = 0.5, col = fcol)
}
else if (isTRUE(fstyle == "bold") == TRUE) {
graphics::text(ndss, labels = as.expression(lapply(lbs,
function(x) bquote(bold(.(x))))), cex = fsize,
adj = 0.5, col = fcol)
}
else if (isTRUE(fstyle == "bolditalic") ==
TRUE) {
graphics::text(ndss, labels = as.expression(lapply(lbs,
function(x) bquote(bolditalic(.(x))))),
cex = fsize, adj = 0.5, col = fcol)
}
}
}
else {
if (missing(fstyle) == TRUE || (missing(fstyle) ==
FALSE && isTRUE(fstyle %in% c("italic", "bold",
"bolditalic") == FALSE))) {
graphics::text(ndss, lbs, cex = fsize, pos = pos[1],
col = fcol, offset = (cex/4L), adj = c(0.5,
1))
}
else if (missing(fstyle) == FALSE) {
if (isTRUE(fstyle == "italic") == TRUE) {
graphics::text(ndss, as.expression(lapply(lbs,
function(x) bquote(italic(.(x))))), cex = fsize,
pos = pos[1], col = fcol, offset = (cex/4L),
adj = c(0.5, 1))
}
else if (isTRUE(fstyle == "bold") == TRUE) {
graphics::text(ndss, as.expression(lapply(lbs,
function(x) bquote(bold(.(x))))), cex = fsize,
pos = pos[1], col = fcol, offset = (cex/4L),
adj = c(0.5, 1))
}
else if (isTRUE(fstyle == "bolditalic") ==
TRUE) {
graphics::text(ndss, as.expression(lapply(lbs,
function(x) bquote(bolditalic(.(x))))),
cex = fsize, pos = pos[1], col = fcol,
offset = (cex/4L), adj = c(0.5, 1))
}
}
}
}
}
graphics::par(mar = omr)
graphics::par(bg = obg)
graphics::par(lend = 0)
graphics::par(mai = omi)
}
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