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Modify a Blueprint using Natural Language

modify_blueprint.Rd

[Experimental] Ask a Large Language Model (LLM) to modify an existing blueprint for glycomics or glycoproteomics data analysis. DeepSeek is used by default for backward compatibility. Other ellmer providers can be selected with provider, model, and provider-specific API key configuration.

Usage

modify_blueprint(
  bp,
  description,
  qa_history = NULL,
  exp = NULL,
  group_col = "group",
  model = getOption("glysmith.ai_model", NULL),
  max_retries = 3,
  provider = getOption("glysmith.ai_provider", "deepseek"),
  api_key = getOption("glysmith.ai_api_key", NULL),
  base_url = getOption("glysmith.ai_base_url", NULL)
)

Arguments

bp

A glysmith_blueprint object.

description

A description of how you want to modify the blueprint.

qa_history

Character vector of Q&A pairs from inquire_blueprint().

exp

Optional. A glyexp::experiment() object to provide more context to the LLM.

group_col

The column name of the group variable in the experiment. Default to "group".

model

Model to use. Defaults to getOption("glysmith.ai_model"), or "deepseek-chat" for DeepSeek and the provider default for other providers.

max_retries

Maximum number of retries when the AI output is invalid. Default to 3.

provider

AI provider passed to ellmer. One of "deepseek", "openai", "anthropic", "gemini", "openrouter", or "openai_compatible". Defaults to getOption("glysmith.ai_provider", "deepseek").

api_key

API key for the selected provider. If NULL, the provider specific environment variable is used. Defaults to getOption("glysmith.ai_api_key").

base_url

Optional base URL for custom or OpenAI-compatible endpoints. Defaults to getOption("glysmith.ai_base_url").

Details

LLMs can be unstable. If you get an error, try again with another description. Make sure to examine the returned blueprint carefully to ensure it's what you want. This function is a companion of inquire_blueprint(). If the LLM needs required information to proceed, it may ask clarifying questions interactively and then retry with your answers.