R code used to produce the graph shown below.
plot(fit, main="")
biplot2 <- function (x, choices = 1L:2L, scale = 1, pc.biplot = FALSE, ...)
{
if (length(choices) != 2L)
stop("length of choices must be 2")
if (!length(scores <- x$x))
stop(gettextf("object '%s' has no scores", deparse(substitute(x))),
domain = NA)
if (is.complex(scores))
stop("biplots are not defined for complex PCA")
lam <- x$sdev[choices]
n <- NROW(scores)
lam <- lam * sqrt(n)
if (scale < 0 || scale > 1)
warning("'scale' is outside [0, 1]")
if (scale != 0)
lam <- lam^scale
else lam <- 1
if (pc.biplot)
lam <- lam/sqrt(n)
biplot.default2(t(t(scores[, choices])/lam), t(t(x$rotation[,
choices]) * lam), ...)
invisible()
}
biplot.default2 <- function(x, y, var.axes = TRUE, col, cex = rep(par("cex"), 2),
xlabs = NULL, ylabs = NULL, expand = 1, xlim = NULL, ylim = NULL,
arrow.len = 0.1, main = NULL, sub = NULL, xlab = NULL, ylab = NULL,
...)
{
n <- nrow(x)
p <- nrow(y)
if (missing(xlabs)) {
xlabs <- dimnames(x)[[1L]]
if (is.null(xlabs))
xlabs <- 1L:n
}
xlabs <- as.character(xlabs)
dimnames(x) <- list(xlabs, dimnames(x)[[2L]])
if (missing(ylabs)) {
ylabs <- dimnames(y)[[1L]]
if (is.null(ylabs))
ylabs <- paste("Var", 1L:p)
}
ylabs <- as.character(ylabs)
dimnames(y) <- list(ylabs, dimnames(y)[[2L]])
if (length(cex) == 1L)
cex <- c(cex, cex)
if (missing(col)) {
col <- par("col")
if (!is.numeric(col))
col <- match(col, palette(), nomatch = 1L)
col <- c(col, col + 1L)
}
else if (length(col) == 1L)
col <- c(col, col)
unsigned.range <- function(x) c(-abs(min(x, na.rm = TRUE)),
abs(max(x, na.rm = TRUE)))
rangx1 <- unsigned.range(x[, 1L])
rangx2 <- unsigned.range(x[, 2L])
rangy1 <- unsigned.range(y[, 1L])
rangy2 <- unsigned.range(y[, 2L])
if (missing(xlim) && missing(ylim))
xlim <- ylim <- rangx1 <- rangx2 <- range(rangx1, rangx2)
else if (missing(xlim))
xlim <- rangx1
else if (missing(ylim))
ylim <- rangx2
ratio <- max(rangy1/rangx1, rangy2/rangx2)/expand
on.exit(par(op))
op <- par(pty = "s")
if (!is.null(main))
op <- c(op, par(mar = par("mar") + c(0, 0, 1, 0)))
plot(x, type = "n", xlim = xlim, ylim = ylim, col = col[1L],
xlab = xlab, ylab = ylab, sub = sub, main = main, ...)
text(x, xlabs, cex = cex[1L], col = col[1L], ...)
par(new = TRUE)
dev.hold()
on.exit(dev.flush(), add = TRUE)
plot(y, axes = FALSE, type = "n", xlim = xlim * ratio, ylim = ylim *
ratio, xlab = "", ylab = "", col = col[1L], ...)
axis(3, col = col[2L], ...)
axis(4, col = col[2L], ...)
box(col = col[1L])
text(y, labels = ylabs, cex = cex[2L], col = col[2L], ...)
if (var.axes)
arrows(0, 0, y[, 1L] * 0.8, y[, 2L] * 0.8, col = col[2L],
length = arrow.len, ...)
invisible()
}
biplot2(fit, cex=mycex, col=c("gray", "blue"), lwd=5)