gptbioinsightor.depict_pathway

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gptbioinsightor.depict_pathway#

gptbioinsightor.depict_pathway(input: dict, out: Path | str | None = None, celltype_dic: dict | None = None, background: str | None = None, database: str | None = None, topnumber: int = 15, n_jobs: int | None = None, provider: str | None = None, model: str | None = None, base_url=None, lang: str = 'en')#

interpret GO term or pathway with actual biological context using LLM.

Parameters:

  • input (dict) – pathway input

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

  • celltype_dic (dict, optional) – celltype of pathway, by default None

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

  • database (str, optional) – pathway database, by default None

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

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

  • provider (str | None, optional) – LLM provider, by default None “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 (_type_, optional) – customized LLM API url, by default None

  • sys_prompt (bool, optional) – use system prompt, by default True

  • lang (str, optional) – language setting, by default “en”

Returns:

None

Return type:

_type_

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