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Run stabilised (multi-run) NMF on single cell or meta cell data

stabilised_nmf_sc.Rd

Runs n_runs HALS NMF with random initialisations seeded by seed + i. The nmf_init field in nmf_hals_params is ignored; random init is always used.

Usage

stabilised_nmf_sc(
  object,
  k,
  cell_ids = NULL,
  gene_ids = NULL,
  preprocessing = "none",
  use_second_layer = TRUE,
  nmf_hals_params = params_nmf_hals(),
  n_runs = 30L,
  seed = 42L,
  .verbose = TRUE
)

Arguments

object

SingleCells or MetaCells class.

k

Integer. Number of latent factors to return.

cell_ids

Optional character. Cell ids (or meta cell ids) to restrict the NMF to. If NULL, uses get_cells_to_keep() for SingleCells and all meta cells for MetaCells.

gene_ids

Optional character. Gene ids to restrict the NMF to. If NULL, uses get_hvg() on the object.

preprocessing

String. One of c("none", "sd", "sqrt_sd").

use_second_layer

Boolean. If TRUE, runs NMF on the normalised counts (recommended); if FALSE, on the raw counts.

nmf_hals_params

List, see params_nmf_hals().

n_runs

Integer. Number of random restarts.

seed

Integer. Random seed for initialisation.

.verbose

Boolean or integer. Verbosity.

Value

A StabilisedNmfResult object.

Examples

# five random restarts, the best one reported
sc <- demo_single_cells()
res <- stabilised_nmf_sc(sc, k = 3L, n_runs = 5L, .verbose = FALSE)
res
#> StabilisedNmfResult (multi-run HALS NMF)
#>   Source class:     SingleCells
#>   No genes:         30
#>   No cells:         500
#>   No components:    3
#>   No runs:          5
#>   No converged:     5 / 5
#>   Loss range:       [5.94e+04, 5.941e+04]
#>   Best run:         3 (loss = 5.94e+04)
#>   Preprocessing:    none

unlink(sc@dir_data, recursive = TRUE, force = TRUE)