gptbioinsightor.get_subtype

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gptbioinsightor.get_subtype#

gptbioinsightor.get_subtype(input, out: Path | str | None = None, celltype: str = None, background: str = None, group: Iterable[str] | None = None, key: str = 'rank_genes_groups', topnumber: int = 15, n_jobs: int | None = None, provider: str = 'openai', model: str | None = None, base_url: str | None = None, rm_genes=True) → dict#

Annotating cell subtypes using LLM, providing cell types, supporting gene markers, reasons, and potential cell state annotations.

Parameters:

  • input (_type_) – An AnnData object or geneset dict

  • out (Path | str | None, optional) – output path, by default None

  • celltype (str, optional) – major cell type, by default None

  • background (str, optional) – background information of input data, by default None

  • group (Iterable[str] | None, optional) – which group, by default None

  • key (str, optional) – deg group key, by default “rank_genes_groups”

  • topnumber (int, optional) – select top gene for analysis, by default 15

  • n_jobs (int | None, optional) – set multiple jobs for querying LLM, by default None

  • provider (str, optional) – LLM provider, by default “openai” “openai” for chatgpt “aliyun” for qwen “moonshot” for kimi

  • model (str | None, optional) – set a model based on LLM provider, by default None

  • base_url (str | None, optional) – customized LLM API url, by default None

  • rm_genes (bool, optional) – remove rb and mt genes, by default True

Returns:

a cell subtypes dict

Return type:

dict

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