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"
}