Nothing
# plot method for all smacof objects
plot.smacof <- function(x, plot.type = "confplot", plot.dim = c(1,2), sphere = TRUE, bubscale = 1,
col = 1, label.conf = list(label = TRUE, pos = 3, col = 1, cex = 0.8),
hull.conf = list(hull = FALSE, col = 1, lwd = 1, ind = NULL),
shepard.x = NULL, identify = FALSE, type = "p", pch = 20, cex = 0.5, asp = 1,
main, xlab, ylab, xlim, ylim, col.hist = NULL, ...)
# x ... object of class smacof
# plot.type ... types available: "confplot", "Shepard", "resplot", "histogram"
# sphere ... if TRUE, sphere is drawn for spherical smacof
{
## --- check type args:
plot.type <- match.arg(plot.type, c("confplot", "Shepard", "resplot","bubbleplot", "stressplot", "histogram"), several.ok = FALSE)
## --- check label lists
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$label <- FALSE
## --- check hull list
if (is.null(hull.conf$hull)) hull.conf$hull <- FALSE
if (is.null(hull.conf$col)) hull.conf$col <- 1
if (is.null(hull.conf$lwd)) hull.conf$lwd <- 1
if (is.null(hull.conf$ind)) hull.conf$ind <- NULL
if (hull.conf$hull && is.null(hull.conf$ind)) stop("Index vector for hulls needs to be specified!")
#--------------- utility function for circle drawing -----------------
circle <- function(x, y, r, ...) {
ang <- seq(0, 2*pi, length = 100)
xx <- x + r * cos(ang)
yy <- y + r * sin(ang)
polygon(xx, yy, ...)
}
#------------ end utility functions ----------------
x1 <- plot.dim[1]
y1 <- plot.dim[2]
#----------------- configuration plot ---------------------
if (plot.type == "confplot") {
#if (type == "n") label.conf$pos <- NULL
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
if (missing(xlim)) xlim <- range(x$conf[,x1])*1.1
if (missing(ylim)) ylim <- range(x$conf[,y1])*1.1
#if (missing(type)) type <- "n" else type <- type
#if (identify) type <- "p"
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, cex = cex, ...)
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 = 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$col)
}
if (hull.conf$hull) {
ind <- hull.conf$ind
n <- dim(x$conf)[1]
M <- as.data.frame(x$conf)
XX <- cbind(M, ind)
X.sort <- XX[order(ind), ]
xx <- yy <- NULL
k <- 0
for (i in 1:n) {
v <- X.sort$ind[i+1]
if (i==n) v="$"
if (X.sort$ind[i] == v ) {
k<-k+1
} else {
von <- i-k
xx <- X.sort[von:i, 1]
yy <- X.sort[von:i, 2]
hpts <- chull(x = xx, y = yy)
hpts <- c(hpts, hpts[1])
lines(xx[hpts], yy[hpts], col = hull.conf$col, lwd = hull.conf$lwd)
k<-0
}
}
}
}
#---------------- Shepard diagram ------------------
if (plot.type == "Shepard") {
if (missing(main)) main <- paste("Shepard Diagram") else main <- main
if (missing(xlab)) {
if (is.null(shepard.x)) xlab <- "Dissimilarities" else xlab <- "Proximities"
} else xlab <- xlab
if (missing(ylab)) ylab <- "Configuration Distances" else ylab <- ylab
notmiss <- as.vector(x$weightmat > 0)
if (is.null(shepard.x)) {
xcoor <- as.vector(x$delta)
} else {
xcoor <- as.vector(as.dist(shepard.x))
}
if (missing(xlim)) xlim <- range(xcoor[notmiss], na.rm = TRUE)
if (missing(ylim)) {
ylim <- range(as.vector(x$confdist)[notmiss])
ylim[1] <- 0
}
plot(xcoor[notmiss], as.vector(x$confdist)[notmiss], main = main, type = "p", pch = pch, cex = cex,
xlab = xlab, ylab = ylab, col = "darkgray", xlim = xlim, ylim = ylim, ...)
notmiss.iord <- notmiss[x$iord]
points((xcoor[x$iord])[notmiss.iord], (as.vector(x$dhat[x$iord]))[notmiss.iord], type = "b", pch = pch, cex = cex)
#points(as.vector(x$delta[x$iord]),as.vector(x$dhat[x$iord]), type = "b", pch = 20, cex = .5)
}
#--------------- Residual plot --------------------
if (plot.type == "resplot") {
if (missing(main)) main <- paste("Residual plot") else main <- main
if (missing(xlab)) xlab <- "Normalized Dissimilarities (d-hats)" else xlab <- xlab
if (missing(ylab)) ylab <- "Configuration Distances" else ylab <- ylab
#resmat <- residuals(x)
if (missing(xlim)) xlim <- range(c(0, as.vector(x$dhat)))
if (missing(ylim)) ylim <- range(c(0, as.vector(x$confdist)))
plot(as.vector(x$dhat), as.vector(x$confdist), main = main, type = "p", col = "darkgray",
xlab = xlab, ylab = ylab, xlim = xlim, ylim = ylim,...)
abline(0, 1)
}
#----------------------- Stress decomposition -----------------
if (plot.type == "stressplot") {
if (missing(main)) main <- paste("Stress Decomposition Chart") else main <- main
if (missing(xlab)) xlab <- "Objects" else xlab <- xlab
if (missing(ylab)) ylab <- "Stress Proportion (%)" else ylab <- ylab
spp.perc <- sort(x$spp, decreasing = TRUE)
xaxlab <- names(spp.perc)
if (missing(xlim)) xlim1 <- c(1,length(spp.perc)) else xlim1 <- xlim
if (missing(ylim)) ylim1 <- (range(spp.perc)*c(0.9, 1.1)) else ylim1 <- ylim
op <- par(mar = c(3, 4, 4, 2))
plot(1:length(spp.perc), spp.perc, xaxt = "n", type = "p", xlab = " ", ylab = ylab, main = main, xlim = xlim1, ylim = ylim1, ...)
mtext(xlab, side = 1, padj = 2)
text(1:length(spp.perc), spp.perc, labels = xaxlab, pos = 3, cex = 0.8)
for (i in 1:length(spp.perc)) lines(c(i,i), c(spp.perc[i],0), col = "lightgray", lty = 2)
par(op)
}
#------------------------------ bubble plot -------------------------
if (plot.type == "bubbleplot")
{
if (missing(main)) main <- paste("Bubble Plot") else main <- main
if (missing(xlab)) xlab <- paste("Dimension", x1,sep = " ") else xlab <- xlab
if (missing(ylab)) ylab <- paste("Dimension", y1,sep = " ") else ylab <- ylab
if (missing(xlim)) xlim <- range(x$conf[,x1])*1.1
if (missing(ylim)) ylim <- range(x$conf[,y1])*1.1
spp.perc <- x$spp
bubsize <- spp.perc/length(spp.perc)*(bubscale + 3)
plot(x$conf, cex = bubsize, main = main, xlab = xlab, ylab = ylab, xlim = xlim, ylim = ylim, asp = asp, ...)
xylabels <- x$conf
ysigns <- sign(x$conf[,y1])
xylabels[,2] <- (abs(x$conf[,y1])-(x$conf[,y1]*(bubsize/50)))*ysigns
text(xylabels, rownames(x$conf), pos = 3,cex = 0.7)
}
#------------------------------ histogram plot -------------------------
if (plot.type == "histogram")
{
if (missing(main)) main <- paste("Weighted histogram") else main <- main
if (missing(xlab)) xlab <- paste("Dissimilarity") else xlab <- xlab
if (missing(ylab)) ylab <- paste("Frequency") else ylab <- ylab
#if (missing(xlim)) xlim <- range(breaks)
wtd.hist(x$delta, weight = x$weightmat, main = main, xlab = xlab, ylab = ylab, col = col.hist, ...)
}
}
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