ccc
Analyze cell-cell communication using methods like cellphonedb, cellchat, or connectome. Group cells by annotations, filter results by expression, and identify ligand-receptor interactions.
Instructions
Cell-cell communication analysis with one method (cellphonedb, cellchat,connectome, natmi, etc.)
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| base | No | Exponent base used to reverse the log-transformation of the matrix. Relevant only for the `logfc` method. | |
| de_method | No | Differential expression method used to rank genes according to 1vsRest. | t-test |
| expr_prop | No | Minimum expression proportion for the ligands and receptors in the corresponding cell identities. Set to 0 to return unfiltered results. | |
| groupby | Yes | Key to be used for grouping cells (e.g., cell type annotations). | |
| inplace | No | Whether to store results in place, or return them. | |
| key_added | No | Key under which the results will be stored in adata.uns. | liana_res |
| layer | No | Layer in AnnData.layers to use. If None, use AnnData.X. | |
| method | No | cell-cell communication method | cellphonedb |
| min_cells | No | Minimum cells per cell identity to be considered for downstream analysis. | |
| n_jobs | No | Number of jobs to run in parallel. | |
| n_perms | No | Number of permutations for the permutation test. Relevant for CellPhoneDB method. | |
| resource_name | No | Name of the resource to be used for ligand-receptor inference. See `li.rs.show_resources()` for available resources. | consensus |
| return_all_lrs | No | Whether to return all ligand-receptor pairs, or only those that surpass the expr_prop threshold. | |
| seed | No | Random seed for reproducibility. | |
| supp_columns | No | Additional columns to be added from methods in liana, or columns from scanpy.tl.rank_genes_groups. | |
| use_raw | No | Use raw attribute of adata if present. | |
| verbose | No | Whether to print verbose output. |
Input Schema (JSON Schema)
{
"description": "Input schema for LIANA's cell-cell communication analysis.",
"properties": {
"base": {
"default": 2.718281828459045,
"description": "Exponent base used to reverse the log-transformation of the matrix. Relevant only for the `logfc` method.",
"title": "Base",
"type": "number"
},
"de_method": {
"default": "t-test",
"description": "Differential expression method used to rank genes according to 1vsRest.",
"title": "De Method",
"type": "string"
},
"expr_prop": {
"default": 0.1,
"description": "Minimum expression proportion for the ligands and receptors in the corresponding cell identities. Set to 0 to return unfiltered results.",
"title": "Expr Prop",
"type": "number"
},
"groupby": {
"description": "Key to be used for grouping cells (e.g., cell type annotations).",
"title": "Groupby",
"type": "string"
},
"inplace": {
"default": true,
"description": "Whether to store results in place, or return them.",
"title": "Inplace",
"type": "boolean"
},
"key_added": {
"default": "liana_res",
"description": "Key under which the results will be stored in adata.uns.",
"title": "Key Added",
"type": "string"
},
"layer": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Layer in AnnData.layers to use. If None, use AnnData.X.",
"title": "Layer"
},
"method": {
"default": "cellphonedb",
"description": "cell-cell communication method",
"enum": [
"singlecellsignalr",
"connectome",
"cellphonedb",
"natmi",
"logfc",
"cellchat",
"geometric_mean",
"scseqcomm"
],
"title": "Method",
"type": "string"
},
"min_cells": {
"default": 5,
"description": "Minimum cells per cell identity to be considered for downstream analysis.",
"title": "Min Cells",
"type": "integer"
},
"n_jobs": {
"default": 1,
"description": "Number of jobs to run in parallel.",
"title": "N Jobs",
"type": "integer"
},
"n_perms": {
"default": 1000,
"description": "Number of permutations for the permutation test. Relevant for CellPhoneDB method.",
"title": "N Perms",
"type": "integer"
},
"resource_name": {
"default": "consensus",
"description": "Name of the resource to be used for ligand-receptor inference. See `li.rs.show_resources()` for available resources.",
"title": "Resource Name",
"type": "string"
},
"return_all_lrs": {
"default": false,
"description": "Whether to return all ligand-receptor pairs, or only those that surpass the expr_prop threshold.",
"title": "Return All Lrs",
"type": "boolean"
},
"seed": {
"default": 1337,
"description": "Random seed for reproducibility.",
"title": "Seed",
"type": "integer"
},
"supp_columns": {
"anyOf": [
{
"items": {
"type": "string"
},
"type": "array"
},
{
"type": "null"
}
],
"default": null,
"description": "Additional columns to be added from methods in liana, or columns from scanpy.tl.rank_genes_groups.",
"title": "Supp Columns"
},
"use_raw": {
"anyOf": [
{
"type": "boolean"
},
{
"type": "null"
}
],
"default": true,
"description": "Use raw attribute of adata if present.",
"title": "Use Raw"
},
"verbose": {
"anyOf": [
{
"type": "boolean"
},
{
"type": "null"
}
],
"default": false,
"description": "Whether to print verbose output.",
"title": "Verbose"
}
},
"required": [
"groupby"
],
"title": "CCCModel",
"type": "object"
}