Fast PCA using irlba.

Fast PCA using irlba.

Usage

runPCA(
  spe,
  n_pcs = 50,
  assay = "logcounts",
  centre = TRUE,
  scale = TRUE,
  name = "PCA",
  ...
)

Arguments

spe

A SpatialExperiment object.

n_pcs

Number of principal components to calculate

assay

Name of assay used for PCA. See details for defaults.

centre

Logical. Whether to centre the assay before PCA.

scale

Logical. Whether to scale the variance to 1 before PCA.

name

Name to store the PCA in the spe's reducedDims

...

Other parameters to be passed to irlba.

Value

A SpatialExperiment with the PCA stored in reducedDims.

Details

By default, runPCA uses logcounts assay (from normalizeAssay). If that's unavailable, it falls back to counts assay

Examples

data("xenium_bc_spe")

spe <- runPCA(spe)
#> Default assay logcounts not found. Switching to counts assay instead.
#> Genes with 0 variance are excluded: ENSG00000135218 NegControlProbe_00002 NegControlCodeword_0504 NegControlCodeword_0509 NegControlCodeword_0510 NegControlCodeword_0511 NegControlCodeword_0512 NegControlCodeword_0516 NegControlCodeword_0517 NegControlCodeword_0518 NegControlCodeword_0519 NegControlCodeword_0520 NegControlCodeword_0522 NegControlCodeword_0526 NegControlCodeword_0527 NegControlCodeword_0530 NegControlCodeword_0536 NegControlCodeword_0537 BLANK_0030 BLANK_0163 BLANK_0165 BLANK_0212 BLANK_0221 BLANK_0230 BLANK_0237 BLANK_0311 BLANK_0361 BLANK_0365 BLANK_0382 BLANK_0384 BLANK_0387 BLANK_0388 BLANK_0391 BLANK_0393 BLANK_0397 BLANK_0399 BLANK_0404 BLANK_0406 BLANK_0410 BLANK_0411 BLANK_0418 BLANK_0425 BLANK_0432 BLANK_0447