Run multiple NMF (HALS) restarts over a set of single cells and genes

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. The returned w_all is the column-binding of all run W matrices.

Usage

rs_nmf_multi_sc(
  f_path_gene,
  gene_indices,
  cell_indices,
  k,
  preprocessing,
  use_second_layer,
  nmf_hals_params,
  n_runs,
  seed,
  verbose
)

Arguments

f_path_gene: Path to the counts_genes.bin file.
gene_indices: Integer vector. 0-indexed(!) positions of the genes to include.
cell_indices: Integer vector. 0-indexed(!) positions of cells to include in the analysis.
k: Integer. Number of latent factors per run.
preprocessing: String. One of c("none", "sd", "sqrt_sd").
use_second_layer: Boolean. If TRUE, runs NMF on the normalised counts; if FALSE, on the raw counts.
nmf_hals_params: Named list. Contains the NMF parameters.
n_runs: Integer. Number of random restarts.
seed: Integer. Base random seed. Run i uses seed + i.
verbose: Integer. 0L - quiet; 1L - normal verbosity; 2L - detailed verbosity.

Value

A list with the following items

w_all - Column-bound W matrices across all runs, shape n_cells x (k * n_runs). Columns i*k+1..(i+1)*k are run i's components (1-indexed).
h_per_run - List of H matrices, each k x n_genes.
losses - Numeric vector. Final reconstruction loss per run.
converged - Logical vector. Convergence flag per run.
best_idx - Integer. 1-indexed position of the run with the lowest final loss.