ATAC API¶

The ATAC branch replaces RNA-style log-normalization with TF-IDF + LSI. Preprocessing and cell typing are ATAC-specific; the sample embedding is shared with RNA.

Function	Purpose
`preprocess` (ATAC)	TF-IDF normalization, LSI projection, optional doublet detection, Harmony on LSI. Drops the first LSI component (depth-correlated) by default. Imported as `from sampledisco.preparation.atac_preprocess_cpu import preprocess`.
`cell_types_atac` (ATAC)	Leiden cell typing on the ATAC DR embedding, with dendrogram / differential-peak analysis. Imported as `from sampledisco.preparation.ATAC_cell_type import cell_types_atac`.

Shared with RNA¶

compute_sample_embedding — the single, unified sample-embedding entry point for RNA, ATAC, and multi-omics (from sampledisco.sample_embedding import compute_sample_embedding). It writes the final sample embedding to adata.uns['X_DR_sample']; there is no longer an atac=True flag.
run_autotune — parameter selection for the sample embedding (from sampledisco.parameter_selection.autotune import run_autotune). It optimizes the RMD-weight alpha (composition vs displacement), enabled via the atac_autotune_enable flag in the config-driven wrapper.

Typical order¶

preprocess (ATAC)
   └─> cell_types_atac                # ATAC-specific cell typing
          └─> compute_sample_embedding
                 └─> downstream analyses

The supported way to run this end-to-end is the config-driven wrapper:

sampledisco -m complex --config config.yaml

For a runnable walkthrough, see the ATAC tutorial.