R - how to make PCA biplot more readable

Question

I have a set of observations with 23 variables.

When I use prcomp and biplot to plot the results I run into several problems:

1. the actual plot only occup

Answer 1

I think you can use xlim and ylim. Also, have a look at the expand argument for ?biplot. Unfortunately, you did not provide any data, so let's take some sample data:

a <- princomp(USArrests)

Below the result of just calling biplot:

biplot(a)

And now one can "zoom in" to have a closer look at "Murder" and "Rape" using xlim and ylim and also use the scaling argument expand from ?biplot:

biplot(a, expand=10, xlim=c(-0.30, 0.0), ylim=c(-0.1, 0.1))

Please note the different scaling on the top and right axis due to the expand factor.

Does this help to make your plot mare readable?

EDIT

You also asked whether it is possible to have different colors for labels and arrows. biplot does not support this, what you could do is to copy the code of stats:::biplot.default and then change it according to your needs (change col argument when plot, axis and text is used).

Alternatively, you could use ggplot for the biplot. In the post here, a simple biplot function is implemented. You could change the code as follows:

PCbiplot <- function(PC, x="PC1", y="PC2", colors=c('black', 'black', 'red', 'red')) {
    # PC being a prcomp object
    data <- data.frame(obsnames=row.names(PC$x), PC$x)
    plot <- ggplot(data, aes_string(x=x, y=y)) + geom_text(alpha=.4, size=3, aes(label=obsnames), color=colors[1])
    plot <- plot + geom_hline(aes(0), size=.2) + geom_vline(aes(0), size=.2, color=colors[2])
    datapc <- data.frame(varnames=rownames(PC$rotation), PC$rotation)
    mult <- min(
        (max(data[,y]) - min(data[,y])/(max(datapc[,y])-min(datapc[,y]))),
        (max(data[,x]) - min(data[,x])/(max(datapc[,x])-min(datapc[,x])))
        )
    datapc <- transform(datapc,
            v1 = .7 * mult * (get(x)),
            v2 = .7 * mult * (get(y))
            )
    plot <- plot + coord_equal() + geom_text(data=datapc, aes(x=v1, y=v2, label=varnames), size = 5, vjust=1, color=colors[3])
    plot <- plot + geom_segment(data=datapc, aes(x=0, y=0, xend=v1, yend=v2), arrow=arrow(length=unit(0.2,"cm")), alpha=0.75, color=colors[4])
    plot
}

Plot as follows:

fit <- prcomp(USArrests, scale=T)
PCbiplot(fit, colors=c("black", "black", "red", "yellow"))

If you play around a bit with this function, I am sure you can figure out how to set xlim and ylim values, etc.