dendrogram

Generate hierarchical clustering dendrograms for single-cell RNA sequencing data. Group observations, specify correlation methods, and customize clustering parameters to visualize relationships in SCMCP MCP server.

Instructions

Hierarchical clustering dendrogram

Input Schema

Name	Required	Description	Default
`cor_method`	No	Correlation method to use: 'pearson', 'kendall', or 'spearman'.	pearson
`groupby`	Yes	The categorical observation annotation to use for grouping.
`key_added`	No	By default, the dendrogram information is added to .uns[f'dendrogram_{groupby}'].
`linkage_method`	No	Linkage method to use for hierarchical clustering.	complete
`n_pcs`	No	Use this many PCs. If n_pcs==0 use .X if use_rep is None.
`optimal_ordering`	No	Reorders the linkage matrix so that the distance between successive leaves is minimal.
`use_raw`	No	Only when var_names is not None. Use raw attribute of adata if present.
`use_rep`	No	Use the indicated representation. 'X' or any key for .obsm is valid.
`var_names`	No	List of var_names to use for computing the hierarchical clustering. If provided, use_rep and n_pcs are ignored.

Input Schema (JSON Schema)

{
  "description": "Input schema for the hierarchical clustering dendrogram tool.",
  "properties": {
    "cor_method": {
      "default": "pearson",
      "description": "Correlation method to use: 'pearson', 'kendall', or 'spearman'.",
      "title": "Cor Method",
      "type": "string"
    },
    "groupby": {
      "description": "The categorical observation annotation to use for grouping.",
      "title": "Groupby",
      "type": "string"
    },
    "key_added": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "By default, the dendrogram information is added to .uns[f'dendrogram_{groupby}'].",
      "title": "Key Added"
    },
    "linkage_method": {
      "default": "complete",
      "description": "Linkage method to use for hierarchical clustering.",
      "title": "Linkage Method",
      "type": "string"
    },
    "n_pcs": {
      "anyOf": [
        {
          "minimum": 0,
          "type": "integer"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Use this many PCs. If n_pcs==0 use .X if use_rep is None.",
      "title": "N Pcs"
    },
    "optimal_ordering": {
      "default": false,
      "description": "Reorders the linkage matrix so that the distance between successive leaves is minimal.",
      "title": "Optimal Ordering",
      "type": "boolean"
    },
    "use_raw": {
      "anyOf": [
        {
          "type": "boolean"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Only when var_names is not None. Use raw attribute of adata if present.",
      "title": "Use Raw"
    },
    "use_rep": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Use the indicated representation. 'X' or any key for .obsm is valid.",
      "title": "Use Rep"
    },
    "var_names": {
      "anyOf": [
        {
          "items": {
            "type": "string"
          },
          "type": "array"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "List of var_names to use for computing the hierarchical clustering. If provided, use_rep and n_pcs are ignored.",
      "title": "Var Names"
    }
  },
  "required": [
    "groupby"
  ],
  "title": "DendrogramModel",
  "type": "object"
}

SCMCP

dendrogram

Instructions

Input Schema

Input Schema (JSON Schema)

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