Get diagnostics from a BulkModuleResult — get

Returns one diagnostic by key, or the whole named list if which is NULL. Contents are method-specific: CoReMo stores stability and cluster_quality; Leiden stores resolution_used and modularity; ICA stores ica_meta and stability_scores; DGRDL stores feature_laplacian, sample_laplacian, and the grid-search table; NMF stores final_loss, n_iter, converged, and (for stabilised runs) losses, best_idx.

Usage

get_diagnostics(object, which = NULL)

Arguments

object: A BulkModuleResult.
which: String or NULL. Name of the diagnostic to return. If NULL, returns the whole list.

Value

The requested diagnostic, the named list, or NULL (with warning) if which is not among the stored diagnostic keys.

Examples

# convergence diagnostics of an NMF fit
syn <- synthetic_bulk_cor_matrix()
mat <- log1p(t(syn$counts))
meta <- data.table::data.table(sample_id = rownames(mat))
object <- BulkCoExp(raw_data = mat, meta_data = meta)
object <- preprocess_bulk_coexp(object, hvg = 500L, .verbose = FALSE)
object <- nmf_bulk(object, k = 3L, .verbose = FALSE)
res <- S7::prop(object, "final_results")
names(get_diagnostics(res))
#> [1] "final_loss" "n_iter"     "converged" 
get_diagnostics(res, "converged")
#> [1] TRUE