embedding_density

Analyze cell density within embeddings to identify spatial patterns in single-cell RNA sequencing data. Supports UMAP or custom embeddings, group-based density calculation, and integration into existing analysis workflows.

Instructions

Calculate the density of cells in an embedding

Input Schema

Name	Required	Description	Default
`basis`	No	The embedding over which the density will be calculated. This embedded representation should be found in `adata.obsm['X_[basis]']`.	umap
`components`	No	The embedding dimensions over which the density should be calculated. This is limited to two components.
`groupby`	No	Key for categorical observation/cell annotation for which densities are calculated per category.
`key_added`	No	Name of the `.obs` covariate that will be added with the density estimates.

Input Schema (JSON Schema)

{
  "description": "Input schema for the embedding density calculation tool.",
  "properties": {
    "basis": {
      "default": "umap",
      "description": "The embedding over which the density will be calculated. This embedded representation should be found in `adata.obsm['X_[basis]']`.",
      "title": "Basis",
      "type": "string"
    },
    "components": {
      "anyOf": [
        {
          "items": {
            "type": "string"
          },
          "type": "array"
        },
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "The embedding dimensions over which the density should be calculated. This is limited to two components.",
      "title": "Components"
    },
    "groupby": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Key for categorical observation/cell annotation for which densities are calculated per category.",
      "title": "Groupby"
    },
    "key_added": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Name of the `.obs` covariate that will be added with the density estimates.",
      "title": "Key Added"
    }
  },
  "title": "EmbeddingDensityModel",
  "type": "object"
}

SCMCP

embedding_density

Instructions

Input Schema

Input Schema (JSON Schema)

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