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"
}