examples/example-plot-bigSVD.R

In privefl/bigstatsr: Statistical Tools for Filebacked Big Matrices

set.seed(1)

X <- big_attachExtdata()
svd <- big_SVD(X, big_scale(), k = 10)

# screeplots
plot(svd) # 3 PCs seems "significant"
plot(svd, coeff = 1.5) # larger font for papers

# scores plot
plot(svd, type = "scores") # first 2 PCs
plot(svd, type = "scores", scores = c(1, 3))
plot(svd, type = "scores", scores = 1:4, ncol = 2, coeff = 0.7)
## add color (recall that this return a `ggplot2` object)
class(obj <- plot(svd, type = "scores"))
pop <- rep(c("POP1", "POP2", "POP3"), c(143, 167, 207))
library(ggplot2)
print(obj2 <- obj + aes(color = pop) + labs(color = "Population"))
## change the place of the legend
print(obj3 <- obj2 + theme(legend.position = c(0.82, 0.17)))
## change the title and the labels of the axes
obj3 + ggtitle("Yet another title") + xlab("with an other 'x' label")

# loadings
plot(svd, type = "loadings", loadings = 2)
## all loadings
plot(svd, type = "loadings", loadings = 1:2, coeff = 0.7, ncol = 1)

# Percentage of variance explained by the PCs
# See https://github.com/privefl/bigstatsr/issues/83

# dynamic plots, require the package **plotly**
\dontrun{plotly::ggplotly(obj3)}