Bare fordi. ggbiplot er en lækker pakke. Det kan bare være en lidt frustrerende oplevelse at få den installeret. Der er bøvl med forskellige versioner af R, og når 60 studerende på et kursus alle prøver at installere fra github samtidig, støder man næsen mod begrænsninger i githubs api. Så. Kopier nedenstående, kør det i R, og funktionen ggbiplot er tilgængelig.

```
ggbiplot <- function (pcobj, choices = 1:2, scale = 1, pc.biplot = TRUE,
obs.scale = 1 - scale, var.scale = scale, groups = NULL,
ellipse = FALSE, ellipse.prob = 0.68, labels = NULL, labels.size = 3,
alpha = 1, var.axes = TRUE, circle = FALSE, circle.prob = 0.69,
varname.size = 3, varname.adjust = 1.5, varname.abbrev = FALSE,
...)
{
library(ggplot2)
library(plyr)
library(scales)
library(grid)
stopifnot(length(choices) == 2)
if (inherits(pcobj, "prcomp")) {
nobs.factor <- sqrt(nrow(pcobj$x) - 1)
d <- pcobj$sdev
u <- sweep(pcobj$x, 2, 1/(d * nobs.factor), FUN = "*")
v <- pcobj$rotation
}
else if (inherits(pcobj, "princomp")) {
nobs.factor <- sqrt(pcobj$n.obs)
d <- pcobj$sdev
u <- sweep(pcobj$scores, 2, 1/(d * nobs.factor), FUN = "*")
v <- pcobj$loadings
}
else if (inherits(pcobj, "PCA")) {
nobs.factor <- sqrt(nrow(pcobj$call$X))
d <- unlist(sqrt(pcobj$eig)[1])
u <- sweep(pcobj$ind$coord, 2, 1/(d * nobs.factor), FUN = "*")
v <- sweep(pcobj$var$coord, 2, sqrt(pcobj$eig[1:ncol(pcobj$var$coord),
1]), FUN = "/")
}
else if (inherits(pcobj, "lda")) {
nobs.factor <- sqrt(pcobj$N)
d <- pcobj$svd
u <- predict(pcobj)$x/nobs.factor
v <- pcobj$scaling
d.total <- sum(d^2)
}
else {
stop("Expected a object of class prcomp, princomp, PCA, or lda")
}
choices <- pmin(choices, ncol(u))
df.u <- as.data.frame(sweep(u[, choices], 2, d[choices]^obs.scale,
FUN = "*"))
v <- sweep(v, 2, d^var.scale, FUN = "*")
df.v <- as.data.frame(v[, choices])
names(df.u) <- c("xvar", "yvar")
names(df.v) <- names(df.u)
if (pc.biplot) {
df.u <- df.u * nobs.factor
}
r <- sqrt(qchisq(circle.prob, df = 2)) * prod(colMeans(df.u^2))^(1/4)
v.scale <- rowSums(v^2)
df.v <- r * df.v/sqrt(max(v.scale))
if (obs.scale == 0) {
u.axis.labs <- paste("standardized PC", choices, sep = "")
}
else {
u.axis.labs <- paste("PC", choices, sep = "")
}
u.axis.labs <- paste(u.axis.labs, sprintf("(%0.1f%% explained var.)",
100 * pcobj$sdev[choices]^2/sum(pcobj$sdev^2)))
if (!is.null(labels)) {
df.u$labels <- labels
}
if (!is.null(groups)) {
df.u$groups <- groups
}
if (varname.abbrev) {
df.v$varname <- abbreviate(rownames(v))
}
else {
df.v$varname <- rownames(v)
}
df.v$angle <- with(df.v, (180/pi) * atan(yvar/xvar))
df.v$hjust = with(df.v, (1 - varname.adjust * sign(xvar))/2)
g <- ggplot(data = df.u, aes(x = xvar, y = yvar)) + xlab(u.axis.labs[1]) +
ylab(u.axis.labs[2]) + coord_equal()
if (var.axes) {
if (circle) {
theta <- c(seq(-pi, pi, length = 50), seq(pi, -pi,
length = 50))
circle <- data.frame(xvar = r * cos(theta), yvar = r *
sin(theta))
g <- g + geom_path(data = circle, color = muted("white"),
size = 1/2, alpha = 1/3)
}
g <- g + geom_segment(data = df.v, aes(x = 0, y = 0,
xend = xvar, yend = yvar), arrow = arrow(length = unit(1/2,
"picas")), color = muted("red"))
}
if (!is.null(df.u$labels)) {
if (!is.null(df.u$groups)) {
g <- g + geom_text(aes(label = labels, color = groups),
size = labels.size)
}
else {
g <- g + geom_text(aes(label = labels), size = labels.size)
}
}
else {
if (!is.null(df.u$groups)) {
g <- g + geom_point(aes(color = groups), alpha = alpha)
}
else {
g <- g + geom_point(alpha = alpha)
}
}
if (!is.null(df.u$groups) && ellipse) {
theta <- c(seq(-pi, pi, length = 50), seq(pi, -pi, length = 50))
circle <- cbind(cos(theta), sin(theta))
ell <- ddply(df.u, "groups", function(x) {
if (nrow(x) <= 2) {
return(NULL)
}
sigma <- var(cbind(x$xvar, x$yvar))
mu <- c(mean(x$xvar), mean(x$yvar))
ed <- sqrt(qchisq(ellipse.prob, df = 2))
data.frame(sweep(circle %*% chol(sigma) * ed, 2,
mu, FUN = "+"), groups = x$groups[1])
})
names(ell)[1:2] <- c("xvar", "yvar")
g <- g + geom_path(data = ell, aes(color = groups, group = groups))
}
if (var.axes) {
g <- g + geom_text(data = df.v, aes(label = varname,
x = xvar, y = yvar, angle = angle, hjust = hjust),
color = "darkred", size = varname.size)
}
return(g)
}
```