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## plot method for Procrustes
plot.procr <- function(x, plot.type = "jointplot", plot.dim = c(1,2), main, xlab, ylab, xlim, ylim, asp = 1, pch = 20,
col.X = "cadetblue", col.Y = "gray", col.Yhat = "coral1",
label.conf = list(label = TRUE, pos = 3, cex = 0.8), arrows = TRUE, length = 0.10,
legend = list(plot = TRUE, labels = c("Target", "Testee"), pos = "bottomright"), ...)
{
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 (is.null(legend$plot)) legend$plot <- TRUE
if (is.null(legend$pos)) legend$pos <- "bottomright"
x1 <- plot.dim[1]
y1 <- plot.dim[2]
if (missing(xlab)) xlab <- paste("Dimension", x1,sep = " ") else xlab <- xlab
if (missing(ylab)) ylab <- paste("Dimension", y1,sep = " ") else ylab <- ylab
labels <- rownames(x$X)
if (plot.type == "jointplot") {
if (is.null(legend$labels)) legend$labels <- c("Target", "Testee")
if (missing(main)) main <- paste("Procrustes Configuration Plot") else main <- main
if (missing(xlim)) xlim <- range(c(x$X[,x1], x$Y[,x1]))*1.1
if (missing(ylim)) ylim <- range(c(x$X[,y1], x$Y[,y1]))*1.1
plot(x$X[,x1], x$X[,y1], main = main, xlab = xlab, ylab = ylab, xlim = xlim, ylim = ylim, pch = pch, asp = asp, col = col.X, ...)
points(x$Yhat[,x1], x$Yhat[,y1], col = col.Yhat, pch = pch)
if (label.conf$label) text(x$X[,x1], x$X[,y1], labels = labels, cex = label.conf$cex, pos = label.conf$pos, col = col.X)
if (label.conf$label) text(x$Yhat[,x1], x$Yhat[,y1], labels = labels, cex = label.conf$cex, pos = label.conf$pos, col = col.Yhat)
if (legend$plot) legend(legend$pos, pch = pch, col = c(col.X, col.Yhat), legend = legend$labels)
}
if (plot.type == "transplot") {
if (missing(main)) main <- paste("Procrustes Transformation Plot") else main <- main
if (missing(xlim)) xlim <- range(c(x$Yhat[,x1], x$Y[,x1]))*1.1
if (missing(ylim)) ylim <- range(c(x$Yhat[,y1], x$Y[,y1]))*1.1
if (is.null(legend$labels)) legend$labels <- c("Original", "Transformed")
plot(x$Y[,x1], x$Y[,y1], main = main, xlab = xlab, ylab = ylab, xlim = xlim, ylim = ylim, pch = pch, asp = asp, col = col.Y)#, ...)
points(x$Yhat[,x1], x$Yhat[,y1], col = col.Yhat, pch = pch)
if (label.conf$label) text(x$Y[,x1], x$Y[,y1], labels = labels, cex = label.conf$cex, pos = label.conf$pos, col = col.Y)
if (label.conf$label) text(x$Yhat[,x1], x$Yhat[,y1], labels = labels, cex = label.conf$cex, pos = label.conf$pos, col = col.Yhat)
if (arrows) arrows(x$Y[,1], x$Y[,2], x$Yhat[,1], x$Yhat[,2], length = length, col = col.Y, lwd = 0.8)
if (legend$plot) legend(legend$pos, pch = pch, col = c(col.Y, col.Yhat), legend = legend$labels)
}
}
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