Adjustable PCA plot — plotPCA.san • carnation

Create a PCA plot with specified PCs on x- and y-axis

Usage

plotPCA.san(
  object,
  intgroup = "group",
  pcx,
  pcy,
  pcz = NULL,
  ntop = 500,
  samples = NULL,
  loadings = FALSE,
  loadings_ngenes = 10
)

object: normalized DESeqDataSet object
intgroup: metadata variable to use for grouping samples
pcx: principal component to plot on x-axis
pcy: principal component to plot on y-axis
pcz: principal component to plot on z-axis. If not NULL, function returns a 3-D PCA plot.
ntop: number of most-variable genes to use
samples: vector of sample names to show on plot
loadings: boolean, show gene loadings? Default is FALSE.
loadings_ngenes: integer, # genes to show loadings for (default=10)