Cluster matrix data by UMAP — runUMAP • karyotapR

Analyzes matrix data by UMAP and saves results to reducedDims slot of TapestriObject.

Usage

runUMAP(
  TapestriExperiment,
  alt.exp = "alleleFrequency",
  assay = NULL,
  use.pca.dims = TRUE,
  pca.dims = NULL,
  ...
)

Arguments

TapestriExperiment: TapestriExperiment object
alt.exp: Character, altExp to use, NULL uses top-level/main experiment. Default "alleleFrequency".
assay: Character, assay to use. NULL (default) uses first-indexed assay. Not used when use.pca.dims = TRUE.
use.pca.dims: Logical, if TRUE, uses experiment PCA, otherwise uses assay data. Default TRUE.
pca.dims: Numeric, indices of PCs to use in UMAP. Default NULL.
...: Additional parameters to pass to umap::umap(), e.g. for configuration (see umap::umap.defaults()).

Value

TapestriExperiment with UMAP embeddings saved to reducedDims slot of altExp.

Examples

tap.object <- newTapestriExperimentExample() # example TapestriExperiment object
#> ℹ Moving gRNA probe  to `altExp` slot "grnaCounts".
#> ℹ Moving barcode probe  to `altExp` slot "barcodeCounts".
#> ℹ Moving chrY probe(s) probe_231, probe_232, probe_233, probe_234, probe_235, probe_236, probe_237, probe_238, probe_239, and probe_240 to `altExp` slot "chrYCounts".
tap.object <- runPCA(tap.object, alt.exp = "alleleFrequency")
tap.object <- runUMAP(tap.object, pca.dims = 1:3)
#> ℹ Running UMAP on: alleleFrequency.