calculate_qc_metrics
Calculate quality control metrics for AnnData, including total counts, gene numbers, and percentages of ribosomal and mitochondrial counts, to evaluate single-cell RNA sequencing data.
Instructions
Calculate quality control metrics(common metrics: total counts, gene number, percentage of counts in ribosomal and mitochondrial) for AnnData.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| expr_type | No | Name of kind of values in X. | counts |
| layer | No | If provided, use adata.layers[layer] for expression values instead of adata.X | |
| log1p | No | Set to False to skip computing log1p transformed annotations. | |
| percent_top | No | List of ranks (where genes are ranked by expression) at which the cumulative proportion of expression will be reported as a percentage. | |
| qc_vars | No | Keys for boolean columns of .var which identify variables you could want to control for mark_var tool should be called frist when you want to calculate mt, ribo, hb, and check tool output for var columns | |
| use_raw | No | If True, use adata.raw.X for expression values instead of adata.X | |
| var_type | No | The kind of thing the variables are. | genes |
Input Schema (JSON Schema)
{
"description": "Input schema for the calculate_qc_metrics preprocessing tool.",
"properties": {
"expr_type": {
"default": "counts",
"description": "Name of kind of values in X.",
"title": "Expr Type",
"type": "string"
},
"layer": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "If provided, use adata.layers[layer] for expression values instead of adata.X",
"title": "Layer"
},
"log1p": {
"default": true,
"description": "Set to False to skip computing log1p transformed annotations.",
"title": "Log1P",
"type": "boolean"
},
"percent_top": {
"anyOf": [
{
"items": {
"type": "integer"
},
"type": "array"
},
{
"type": "null"
}
],
"default": [
50,
100,
200,
500
],
"description": "List of ranks (where genes are ranked by expression) at which the cumulative proportion of expression will be reported as a percentage.",
"title": "Percent Top"
},
"qc_vars": {
"anyOf": [
{
"items": {
"type": "string"
},
"type": "array"
},
{
"type": "string"
},
{
"type": "null"
}
],
"default": [],
"description": "Keys for boolean columns of .var which identify variables you could want to control for mark_var tool should be called frist when you want to calculate mt, ribo, hb, and check tool output for var columns",
"title": "Qc Vars"
},
"use_raw": {
"default": false,
"description": "If True, use adata.raw.X for expression values instead of adata.X",
"title": "Use Raw",
"type": "boolean"
},
"var_type": {
"default": "genes",
"description": "The kind of thing the variables are.",
"title": "Var Type",
"type": "string"
}
},
"title": "CalculateQCMetrics",
"type": "object"
}