static visualization of PCA pairs — strat2d • BiocT2T

static visualization of PCA pairs

strat2d(
  pcmat,
  pcinds = 5:8,
  superpop = "AFR",
  GGally = FALSE,
  superOnly = FALSE
)

Arguments

pcmat: matrix with columns PC1...PCn
pcinds: numeric vector with suffixes from colnames(pcmat) to select for visualization
superpop: character(1) three letter superpopulation code, see `data(igsr_pops)`
GGally: logical(1) if TRUE, use `GGally::ggpairs` to visualize, otherwise `pairs()`
superOnly: logical(1) defaults to FALSE; if TRUE, do not limit to one superpopulation

Value

Side effects of plotting with either `pairs` or `GGally`

Examples

data(pc_190kloci)
strat2d(pc_190kloci)