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# plot method for bootstrap smacof
plot.smacofboot <- function(x, plot.dim = c(1,2), col = 1, label.conf = list(label = TRUE, pos = 3, cex = 0.8),
ell = list(lty = 1, lwd = 1, col = "gray"), main, xlab, ylab, xlim, ylim, asp = 1, type = "p", pch = 20, ...)
{
# x ... object of class smacofboot
x1 <- plot.dim[1]
y1 <- plot.dim[2]
if (missing(main)) main <- paste("MDS Bootstrap Plot") else main <- main
if (missing(xlab)) xlab <- paste("Dimension", x1,sep = " ") else xlab <- xlab
if (missing(ylab)) ylab <- paste("Dimension", y1,sep = " ") else ylab <- ylab
if (is.null(label.conf$label)) label.conf$label <- TRUE
if (is.null(label.conf$pos)) label.conf$pos <- 3
if (is.null(label.conf$cex)) label.conf$cex <- 0.8
if (is.null(ell$lty)) ell$lty <- 1
if (is.null(ell$lwd)) ell$lwd <- 1
if (is.null(ell$col)) ell$col <- "gray"
n <- x$nobj
aus <- list()
for (i in 1:n) aus[[i]] <- ellipse(x$cov[[i]][plot.dim, plot.dim], level = 1-x$alpha, type = 'l', centre = x$conf[i,plot.dim])
limcoor <- rbind(do.call(rbind, aus), x$conf[,plot.dim])
if (missing(xlim)) xlim <- range(limcoor[,1])*1.1
if (missing(ylim)) ylim <- range(limcoor[,2])*1.1
plot(x$conf[,x1], x$conf[,y1], main = main, type = type, xlab = xlab, ylab = ylab,
xlim = xlim, ylim = ylim, pch = pch, asp = asp, col = col, ...)
if (label.conf$label) {
if (label.conf$pos == 5) {
thigmophobe.labels(x$conf[,x1], x$conf[,y1], labels = rownames(x$conf),
cex = label.conf$cex, text.pos = NULL,
col = col)
} else {
text(x$conf[,x1], x$conf[,y1], labels = rownames(x$conf),
cex = label.conf$cex, pos = label.conf$pos,
col = col)
}
}
if (length(ell$col) != n) cols <- rep(ell$col[1], n)
for (i in 1:n) lines(aus[[i]][,1], aus[[i]][,2], lty = ell$lty, lwd = ell$lwd, col = cols[i])
names(aus) <- rownames(x$conf)
invisible(aus)
}
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