Output

Output levels

output_level = "standard" is the default. debug keeps the same final result and search trace, then adds the information needed to inspect individual candidate partitions.

Standard (default)

result
├── labels / object
├── selection
└── search_trace

Debug

result
├── labels / object
├── selection
├── search_trace
└── debug

Standard output

Domain labels

Entry point	Result location	Meaning
`bcmp_embedding()`	`result$labels`	Cell-ID-named character vector of BCMP domains.
`bcmp()` on Seurat	`result$object[["bcmp_domain"]]`	Labels in a copied Seurat object.
`bcmp()` on SCE	`colData(result$object)$bcmp_domain`	Labels in a copied SingleCellExperiment object.

Final selection

result$selection describes the final partition:

Name	Meaning
`selected_k`	Representation scale selected by the search.
`n_domains`	Number of domains in the selected partition.
`mixing_status`	`"pass"` or `"fail"` for the selected partition.
`n_evaluated_domains`	Domains used in the mixing decision.
`n_residual_domains` / `n_residual_cells`	Residual domains and their active cells.
`residual_cell_frac`	Fraction of active cells in residual domains.

Search trace

result$search_trace records the k values BCMP tested to choose selected_k; each row is one tested k:

Name	Meaning
`iter_id` / `phase` / `k`	Evaluation order, role (`k_low`, `k_high`, or `k_mid`), and scale.
`mixing_status`	Mixing outcome at that scale.
`n_domains` / `n_failed_domains` / `n_residual_domains`	Domain counts at that scale.
`actual_residual_cell_frac`	Observed active-cell fraction in residual domains.

Debug output

Debug output explains how the search reached its final result. It retains the standard fields and adds result$debug:

debug
├── parameters
├── search
├── candidates[[k]]
│   ├── partition
│   └── domain_summary
└── workflow                    # object workflows only
    ├── hvg_genes
    └── excluded_cell_ids

The parameters field records the values supplied for the run. search records the resolved k bounds and the final search outcome. Each candidates[[k]] entry corresponds to one tested k in search_trace; partition contains the cell-level domain labels, while domain_summary reports domain size, cell fraction, batch support, and mixing status.

For bcmp(), workflow records the selected hvg_genes and excluded_cell_ids; parameters records the resolved raw-count assay/layer and the supplied preprocessing settings. Debug object results write newly computed BCMP_PCA and BCMP_UMAP reductions in both Seurat v5 and SingleCellExperiment.