PCA example

gistfile1.txt

# PCA: Check for batch effects. Select one batch, to color points by its assignment
pca <-  mtx %>% varFilter(., var.cutoff = 0.75) %>% scale %>% t %>% prcomp

colorby <- "Group" # covariates[2]
pt <- ggplot(data = data.frame(pca$x, annot), 
             aes(x = as.numeric(PC1), y = as.numeric(PC2), label = Sample)) +
  theme(plot.title = element_text(lineheight = 0.8, face="bold")) +
  ggtitle(paste("PCA with batch, coloring by ", colorby)) +
  geom_point(aes(color = eval(parse(text = colorby))), size = 3) +
  geom_text_repel(colour = "black", size = 3) +
  geom_hline(yintercept = 0, colour = "gray65") +
  geom_vline(xintercept = 0, colour = "gray65") +
  labs(color = colorby) +
  scale_x_continuous(name = paste0("PC1, ", round(summary(pca)$importance[2,1] * 100, digits = 2), "% variability" )) +
  scale_y_continuous(name = paste0("PC2, ", round(summary(pca)$importance[2,2] * 100, digits = 2), "% variability" )) +
   theme(legend.position="none")
plot(pt)

ggsave(filename = "Figures/Figure_PCA_withbatch.pdf", plot = pt, height = 8, width = 11)