SCMCP

Instructions

Implementation Reference

• src/scmcp/tool/ccc.py:53-62 (handler)

  Core handler function `run_ccc` that performs the cell-cell communication analysis by dynamically calling the specified LIANA method function.

  def run_ccc(adata, method, **kwargs):
      """Run cell-cell communication analysis with the specified method."""
      method_func = getattr(li.mt, method)
      parameters = inspect.signature(method_func).parameters
      filtered_kwargs = {k: kwargs.get(k) for k in parameters if k in kwargs}
      # filtered_kwargs["key_added"] = f"{method}_res"
      method_func(adata, **filtered_kwargs)
      add_op_log(adata, method_func, filtered_kwargs)
      return adata

• src/scmcp/schema/ccc.py:81-180 (schema)

  Pydantic model defining the input schema for the 'ccc' tool, used in inputSchema=CCCModel.model_json_schema().

  class CCCModel(JSONParsingModel):
      """Input schema for LIANA's cell-cell communication analysis."""
      
      method: Literal[
          "singlecellsignalr", 
          "connectome", 
          "cellphonedb", 
          "natmi", 
          "logfc", 
          "cellchat", 
          "geometric_mean", 
          "scseqcomm"
      ] = Field(
          default="cellphonedb",
          description="cell-cell communication method"
      )
      
      groupby: str = Field(
          ...,  # Required field
          description="Key to be used for grouping cells (e.g., cell type annotations)."
      )
      
      resource_name: str = Field(
          default="consensus",
          description="Name of the resource to be used for ligand-receptor inference. See `li.rs.show_resources()` for available resources."
      )
      
      expr_prop: float = Field(
          default=0.1,
          description="Minimum expression proportion for the ligands and receptors in the corresponding cell identities. Set to 0 to return unfiltered results."
      )
      
      min_cells: int = Field(
          default=5,
          description="Minimum cells per cell identity to be considered for downstream analysis."
      )
      
      base: float = Field(
          default=2.718281828459045,  # e
          description="Exponent base used to reverse the log-transformation of the matrix. Relevant only for the `logfc` method."
      )
      
      return_all_lrs: bool = Field(
          default=False,
          description="Whether to return all ligand-receptor pairs, or only those that surpass the expr_prop threshold."
      )
      
      key_added: str = Field(
          default="liana_res",
          description="Key under which the results will be stored in adata.uns."
      )
      
      use_raw: Optional[bool] = Field(
          default=True,
          description="Use raw attribute of adata if present."
      )
      
      layer: Optional[str] = Field(
          default=None,
          description="Layer in AnnData.layers to use. If None, use AnnData.X."
      )
      
      de_method: str = Field(
          default="t-test",
          description="Differential expression method used to rank genes according to 1vsRest."
      )
      
      n_perms: int = Field(
          default=1000,
          description="Number of permutations for the permutation test. Relevant for CellPhoneDB method."
      )
      
      seed: int = Field(
          default=1337,
          description="Random seed for reproducibility."
      )
      
      n_jobs: int = Field(
          default=1,
          description="Number of jobs to run in parallel."
      )
      
      verbose: Optional[bool] = Field(
          default=False,
          description="Whether to print verbose output."
      )
      
      inplace: bool = Field(
          default=True,
          description="Whether to store results in place, or return them."
      )
      
      supp_columns: Optional[List[str]] = Field(
          default=None,
          description="Additional columns to be added from methods in liana, or columns from scanpy.tl.rank_genes_groups."
      )

• src/scmcp/tool/ccc.py:42-47 (registration)

  Tool object registration for the 'ccc' tool.

  # Add general CCC tool
  ccc_tool = types.Tool(
      name="ccc",
      description="Cell-cell communication analysis with one method (cellphonedb, cellchat,connectome, natmi, etc.)",
      inputSchema=CCCModel.model_json_schema(),
  )

• src/scmcp/tool/ccc.py:100-106 (registration)

  Mapping of 'ccc' tool to ccc_tools dictionary, which is used for registration in server.list_tools().

  ccc_tools = {
      "ls_ccc_method": ls_ccc_method_tool,
      "ccc_rank_aggregate": rank_aggregate_tool,
      "ccc_circle_plot": circle_plot_tool,
      "ccc_dot_plot": dot_plot_tool,
      "ccc": ccc_tool,
  }

• src/scmcp/server.py:35-56 (registration)

  Server tool listing function that includes ccc_tools.values(), registering the 'ccc' tool.

  @server.list_tools()
  async def list_tools() -> list[types.Tool]:
      if MODULE == "io":
          tools = io_tools.values()
      elif MODULE == "pp":
          tools = pp_tools.values()
      elif MODULE == "tl":
          tools = tl_tools.values()
      elif MODULE == "pl":
          tools = pl_tools.values()
      elif MODULE == "util":
          tools = util_tools.values()
      else:
          tools = [
              *io_tools.values(),
              *pp_tools.values(),
              *tl_tools.values(),
              *pl_tools.values(),
              *util_tools.values(),
              *ccc_tools.values(),
          ]
      return tools