scbiot.ot.integrate

scbiot.ot.integrate(adata, obsm_key='X_pca', batch_key='batch', out_key='scBIOT', strength=0.5, conservation=0.5, prototypes=0.5, sharpen=0.5, supervision=0.5, projector=0.5, approximate=False, centroid=False, reference='auto', label_key=None, unlabeled_category='unknown', use_gpu=True, gpu_device=0, ot_backend='torch', random_state=0, verbose=True, modality='auto', spatial_key=None, spatial_weight=0.5, prealign=None, prealign_strength=1.0, prealign_eps=0.01, prealign_max_points=20000, max_iter=15, n_centroids_per_batch=2048, max_samples_per_batch=500000, k_interp=8, chunk_size=500000, tmp_path=None, align_reference=False, run_three_stage=True)

Wrapper around integrate_ot with the same knob-based interface.

If label_key is provided (and exists in adata.obs), this runs an internal three-stage sequence that exactly mimics calling integrate_ot externally as: supervised → unsupervised → supervised, with projector disabled in the two supervised stages. Intermediate embeddings are stored under temporary obsm keys and removed before returning.

Parameters:

• adata (Any)

• obsm_key (str)

• batch_key (str)

• out_key (str)

• strength (float)

• conservation (float)

• prototypes (float)

• sharpen (float)

• supervision (float)

• projector (float)

• approximate (bool)

• centroid (bool)

• reference (str)

• label_key (str | None)

• unlabeled_category (Any)

• use_gpu (bool)

• gpu_device (int)

• ot_backend (str)

• random_state (int)

• verbose (bool)

• modality (str)

• spatial_key (str | None)

• spatial_weight (float)

• prealign (str | None)

• prealign_strength (float)

• prealign_eps (float)

• prealign_max_points (int)

• max_iter (int)

• n_centroids_per_batch (int)

• max_samples_per_batch (int)

• k_interp (int)

• chunk_size (int)

• tmp_path (str | None)

• align_reference (bool)

• run_three_stage (bool)