neighbors

Compute nearest neighbors distance matrices and construct neighborhood graphs for single-cell RNA sequencing data analysis. Supports customizable parameters for manifold approximation, distance metrics, and kNN search methods.

Instructions

Compute nearest neighbors distance matrix and neighborhood graph

Input Schema

Name	Required	Description	Default
`key_added`	No	Key prefix for storing neighbor results.
`knn`	No	Whether to use hard threshold for neighbor restriction.
`method`	No	Method for computing connectivities ('umap' or 'gauss').	umap
`metric`	No	Distance metric to use.	euclidean
`metric_kwds`	No	Options for the distance metric.
`n_neighbors`	No	Size of local neighborhood used for manifold approximation.
`n_pcs`	No	Number of PCs to use. If None, automatically determined.
`random_state`	No	Random seed for reproducibility.
`transformer`	No	Approximate kNN search implementation ('pynndescent' or 'rapids').
`use_rep`	No	Key for .obsm to use as representation.

Input Schema (JSON Schema)

{
  "description": "Input schema for the neighbors graph construction tool.",
  "properties": {
    "key_added": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Key prefix for storing neighbor results.",
      "title": "Key Added"
    },
    "knn": {
      "default": true,
      "description": "Whether to use hard threshold for neighbor restriction.",
      "title": "Knn",
      "type": "boolean"
    },
    "method": {
      "default": "umap",
      "description": "Method for computing connectivities ('umap' or 'gauss').",
      "enum": [
        "umap",
        "gauss"
      ],
      "title": "Method",
      "type": "string"
    },
    "metric": {
      "default": "euclidean",
      "description": "Distance metric to use.",
      "title": "Metric",
      "type": "string"
    },
    "metric_kwds": {
      "additionalProperties": true,
      "description": "Options for the distance metric.",
      "title": "Metric Kwds",
      "type": "object"
    },
    "n_neighbors": {
      "default": 15,
      "description": "Size of local neighborhood used for manifold approximation.",
      "exclusiveMinimum": 1,
      "maximum": 100,
      "title": "N Neighbors",
      "type": "integer"
    },
    "n_pcs": {
      "anyOf": [
        {
          "minimum": 0,
          "type": "integer"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Number of PCs to use. If None, automatically determined.",
      "title": "N Pcs"
    },
    "random_state": {
      "default": 0,
      "description": "Random seed for reproducibility.",
      "title": "Random State",
      "type": "integer"
    },
    "transformer": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Approximate kNN search implementation ('pynndescent' or 'rapids').",
      "title": "Transformer"
    },
    "use_rep": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Key for .obsm to use as representation.",
      "title": "Use Rep"
    }
  },
  "title": "NeighborsModel",
  "type": "object"
}

SCMCP

neighbors

Instructions

Input Schema

Input Schema (JSON Schema)

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