pca.R

library(mia)
library(microbiomeDataSets)

x <- atlas1006()
x <- transformCounts(x, abund_values="counts", method="clr", pseudocount=1)
A <- t(assay(x, "clr"))
As <- scale(A)
pca <- princomp(A)
pca.scaled <- princomp(As)

par(mfrow=c(2, 2))
plot(pca$scores[, 1:2], main="Scores unscaled")
plot(pca.scaled$scores[, 1:2], main="Scores scaled")
barplot(sort(pca$loadings[, 1]), main="Loadings unscaled", horiz=TRUE, las=1)
barplot(sort(pca.scaled$loadings[, 1]), main="Loadings scaled", horiz=TRUE, las=1)