screeplot.R

# create screeplot with PCAtools package
## find optimum number of PCs to retain
elbow <- PCAtools::findElbowPoint(p$variance)
## set image path
image_filepath <- fs::path(data_dir, glue::glue("img/{bmd_tag}.screeplot.png"))
## open image file
png(image_filepath, width=4, height=4, units="in", res=300)
## create image
PCAtools::screeplot(
  p,
  components = PCAtools::getComponents(p, 1:10),
  vline = elbow)
## close devide target of image
dev.off()