(R) Visualizing a data set with large number of variables using PCA (ggbiplot)

Question

My dataset has 100 samples and 17000 variables. I would use PCA and visualize data. But the problem is that the plot is not good. How I can control the number of arrows in ggbiplot or biplot, in fact select the most contributed variables? Some sample codes are as below:

data <- matrix(rnorm(1700000), nrow=100, ncol=17000)
colnames(data) <- paste("X", 1:ncol(data), sep="")
pca <- prcomp(data, scale=T, center=T)

biplot(pca)
print(ggbiplot(pca, obs.scale = 1, var.scale = 1, 
               groups = c(rep('a',30), rep('b',70))))

This is perfectly valid question with a reproducible example. No need to close. — Roman Luštrik, Mar 10 '16 at 13:13

score 2 · Accepted Answer · answered Mar 10 '16 at 13:38

I assumed you got a recent version of ggbiplot from github (19 Jun 2015 https://github.com/vqv/ggbiplot). In this one, I don't think there's a clean way to reduce the number of arrows. You'd have to modify the original function by subsetting the df.v in two plotting calls:

around line 89:

g <- g + geom_segment(data = df.v[1:5,], # SUBSET HERE
aes(x = 0, y = 0, xend = xvar, yend = yvar), arrow = arrow(length = unit(1/2, "picas")), color = muted("red"))

and around line 127:

g <- g + geom_text(data = df.v[1:5,], # SUBSET HERE
aes(label = varname, x = xvar, y = yvar, angle = angle, hjust = hjust), color ="darkred", size = varname.size)

Great!! Thank you so much. – user4704857 Mar 10 '16 at 14:31 — user4704857, Mar 10 '16 at 14:31

(R) Visualizing a data set with large number of variables using PCA (ggbiplot)

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