merge_adata
Combine multiple AnnData objects along specified axes (observations or variables) using customizable alignment and merging strategies. Supports inner and outer joins, index uniqueness, and batch labeling for enhanced single-cell RNA sequencing data integration.
Instructions
merge multiple adata
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| axis | No | Which axis to concatenate along. 'obs' or 0 for observations, 'var' or 1 for variables. | obs |
| fill_value | No | When join='outer', this is the value that will be used to fill the introduced indices. | |
| index_unique | No | Whether to make the index unique by using the keys. If provided, this is the delimiter between '{orig_idx}{index_unique}{key}'. | |
| join | No | How to align values when concatenating. If 'outer', the union of the other axis is taken. If 'inner', the intersection. | inner |
| keys | No | Names for each object being added. These values are used for column values for label or appended to the index if index_unique is not None. | |
| label | No | label different adata, Column in axis annotation (i.e. .obs or .var) to place batch information in. | |
| merge | No | How elements not aligned to the axis being concatenated along are selected. | |
| pairwise | No | Whether pairwise elements along the concatenated dimension should be included. | |
| uns_merge | No | How the elements of .uns are selected. Uses the same set of strategies as the merge argument, except applied recursively. |
Input Schema (JSON Schema)
{
"description": "Model for concatenating AnnData objects",
"properties": {
"axis": {
"default": "obs",
"description": "Which axis to concatenate along. 'obs' or 0 for observations, 'var' or 1 for variables.",
"enum": [
"obs",
0,
"var",
1
],
"title": "Axis"
},
"fill_value": {
"anyOf": [
{},
{
"type": "null"
}
],
"default": null,
"description": "When join='outer', this is the value that will be used to fill the introduced indices.",
"title": "Fill Value"
},
"index_unique": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Whether to make the index unique by using the keys. If provided, this is the delimiter between '{orig_idx}{index_unique}{key}'.",
"title": "Index Unique"
},
"join": {
"default": "inner",
"description": "How to align values when concatenating. If 'outer', the union of the other axis is taken. If 'inner', the intersection.",
"enum": [
"inner",
"outer"
],
"title": "Join",
"type": "string"
},
"keys": {
"anyOf": [
{
"items": {
"type": "string"
},
"type": "array"
},
{
"type": "null"
}
],
"default": null,
"description": "Names for each object being added. These values are used for column values for label or appended to the index if index_unique is not None.",
"title": "Keys"
},
"label": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "label different adata, Column in axis annotation (i.e. .obs or .var) to place batch information in. ",
"title": "Label"
},
"merge": {
"anyOf": [
{
"enum": [
"same",
"unique",
"first",
"only"
],
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "How elements not aligned to the axis being concatenated along are selected.",
"title": "Merge"
},
"pairwise": {
"default": false,
"description": "Whether pairwise elements along the concatenated dimension should be included.",
"title": "Pairwise",
"type": "boolean"
},
"uns_merge": {
"anyOf": [
{
"enum": [
"same",
"unique",
"first",
"only"
],
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "How the elements of .uns are selected. Uses the same set of strategies as the merge argument, except applied recursively.",
"title": "Uns Merge"
}
},
"title": "ConcatAdataModel",
"type": "object"
}