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 / adata
├── selection
└── search_trace

Debug

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

Standard output

Domain labels

Entry point	Result location	Meaning
bcmp(...)	result.adata.obs["bcmp_domain"]	BCMP domain labels in a copied AnnData object. The input AnnData is not modified.
bcmp_embedding(...)	result.labels	A cell-indexed series of BCMP domain labels.

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 is for examining how the search arrived at its result. It retains the standard fields and adds result.debug:

result
├── labels / adata
│           └── obsm
│               ├── X_bcmp_pca
│               └── X_bcmp_umap
├── selection
├── search_trace
└── debug
    ├── parameters
    ├── search
    ├── candidates[k]
    │   ├── partition
    │   └── domain_summary
    └── workflow
        ├── hvg_genes
        └── excluded_cell_ids

The parameters field records the input values used for the run; search records the resolved k bounds and search outcome. Each candidates[k] entry corresponds to one row of search_trace. partition is a cell-indexed domain-label series, while domain_summary reports domain size, cell fraction, batch support, and mixing status.

In debug output from bcmp(...), the additional workflow contains the selected HVG genes and excluded cell IDs; adata.obsm additionally contains the uncorrected PCA in X_bcmp_pca and a diagnostic UMAP in X_bcmp_umap.