omicverse.single.get_cluster_celltype

omicverse.single.get_cluster_celltype(cluster_celltypes, cluster_markers, species, organization, model, base_url, provider, api_key=None, timeout=30, max_retries=2, retry_backoff=1.5, verbose=True)[source]

Resolve one final cell type for each cluster with LLM calls.

Parameters:

  • cluster_celltypes (dict) – Candidate labels per cluster, usually dict[cluster_id -> list[str]].

  • cluster_markers (dict) – Marker genes per cluster, usually dict[cluster_id -> list[str]].

  • species (str) – Species context used in prompt construction.

  • organization (str) – Tissue/organ context used in prompt construction.

  • model (str) – Chat completion model name.

  • base_url (str or None) – API base URL. If None, inferred from provider.

  • provider (str) – Provider preset used for base URL fallback.

  • api_key (str or None, default=None) – Optional API key override. If None, reads AGI_API_KEY.

  • timeout (int, default=30) – Request timeout in seconds for each API call.

  • max_retries (int, default=2) – Maximum retry count for failed requests.

  • retry_backoff (float, default=1.5) – Exponential backoff base for retry waiting time.

  • verbose (bool, default=True) – Whether to print retry/fallback diagnostics.

Returns:

Mapping from cluster ID to predicted (or fallback) cell-type label.

Return type:

dict