UMAP using uwot. Parameters are set to be similar to Seurat's

UMAP using uwot. Parameters are set to be similar to Seurat's

Usage

runUMAP(
  spe,
  n_neighbors = 30,
  n_components = 2,
  metric = "cosine",
  min_dist = 0.3,
  assay = NULL,
  dimred = "PCA",
  n_dimred = NULL,
  name = "UMAP",
  ...
)

Arguments

spe

A SpatialExperiment object.

n_neighbors, n_components, metric, min_dist

See umap

assay

Name of assay for UMAP. Incompatible with dimred.

dimred

Name of the dimensionality reduction (e.g. PCA) for UMAP. Incompatible with assay

n_dimred

Integer scalar or vector specifying the dimensions to use if dimred is specified.

name

Name to store the UMAP in the spe's reducedDims.

...

Other parameters to be passed to umap.

Value

A SpatialExperiment with the UMAP stored in reducedDims.

Details

By default, runUMAP uses PCA (from runPCA). If that's unavailable, it falls back to logcounts, then 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
spe <- runUMAP(spe,dimred="PCA",n_dimred=10)