PCA old

pcaGenes <- function(.data, .cast.freq.seg = T, ..., ..do.plot = T){
  if (.cast.freq.seg) { .data <- freq.segments(.data)[,-1] }
  pca.res <- prcomp(t(as.matrix(.data)), ...)
  if (.do.plot) {
    pca.res <- data.frame(PC1 = pca.res$x[,1], PC2 = pca.res$x[,2], Subject = names(.data))
    ggplot() + geom_point(aes(x = PC1, y = PC2, colour = Subject), size = 3, data = pca.res) +
      theme_linedraw() + guides(size=F) + ggtitle("VJ-usage: Principal Components Analysis")
  } else {
    pca.res
  }
}