Nothing
plot.mdsbi <- function(x, vecscale = NULL, plot.dim = c(1,2), sphere = TRUE, col = 1, label.conf = list(label = TRUE, pos = 3, col = 1, cex = 0.8),
vec.conf = list(col = 1, cex = 0.8, length = 0.1),
identify = FALSE, type = "p", pch = 20,
asp = 1, main, xlab, ylab, xlim, ylim, ...) {
## argument checks
x1 <- plot.dim[1]
y1 <- plot.dim[2]
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$col)) label.conf$col <- 1
if (is.null(label.conf$cex)) label.conf$cex <- 0.8
if (identify) label.conf$label <- FALSE
if (is.null(vec.conf$length)) vec.conf$length <- 0.1
if (is.null(vec.conf$col)) vec.conf$col <- 1
if (is.null(vec.conf$cex)) vec.conf$cex <- 0.8
if (missing(main)) main <- paste("Configuration Plot") else main <- main
if (missing(xlab)) xlab <- paste("Dimension", x1,sep = " ") else xlab <- xlab
if (missing(ylab)) ylab <- paste("Dimension", y1,sep = " ") else ylab <- ylab
circle <- function(x, y, r, ...) {
ang <- seq(0, 2*pi, length = 100)
xx <- x + r * cos(ang)
yy <- y + r * sin(ang)
polygon(xx, yy, ...)
}
x$conf <- x$model$X ## configurations
if (is.null(vecscale) && ncol(x$coef) == 1) vecscale <- 1
if (is.null(vecscale)) vecscale <- vecscale(x$coef) ## scale
x$coef <- vecscale * x$coef
temp <- rbind(x$conf, t(x$coef))
if (missing(xlim)) xlim <- range(temp[,x1])*1.1
if (missing(ylim)) ylim <- range(temp[,y1])*1.1
## configuration plot
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[1] == 5) {
thigmophobe.labels(x$conf[,x1], x$conf[,y1], labels = rownames(x$conf),
cex = label.conf$cex, text.pos = NULL,
col = label.conf$col)
} else {
text(x$conf[,x1], x$conf[,y1], labels = rownames(x$conf),
cex = label.conf$cex, pos = label.conf$pos,
col = label.conf$col)
}
}
if ((any(class(x) == "smacofSP")) && (sphere)) {
radius <- sqrt(x$conf[2,1]^2 + x$conf[2,2]^2)
circle(0, 0, radius, lty = 2, border = "lightgray")
}
if (identify) {
identify(x$conf[,x1], x$conf[,y1], labels = rownames(x$conf), cex = label.conf$cex, pos = label.conf$pos,
col = label.conf$col)
}
## add vectors
abline(h = 0, v = 0, lty = 2, col = "darkgray")
n <- ncol(x$coef)
xycoor <- t(x$coef[c(x1, y1), ])
posvec <- apply(xycoor, 1, sign)[2,] + 2
for (i in 1:n) {
arrows(0, 0, x$coef[x1, i], x$coef[y1, i], length = vec.conf$length, col = vec.conf$col)
text(x$coef[x1, i], x$coef[y1, i], labels = colnames(x$coef)[i], col = vec.conf$col, pos = posvec[i], cex = vec.conf$cex)
}
}
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