scanpy.tl.score_genes

scanpy.tl.score_genes(adata, gene_list, ctrl_size=50, gene_pool=None, n_bins=25, score_name='score', random_state=0, copy=False, use_raw=None)

Score a set of genes [Satija15].

The score is the average expression of a set of genes subtracted with the average expression of a reference set of genes. The reference set is randomly sampled from the gene_pool for each binned expression value.

This reproduces the approach in Seurat [Satija15] and has been implemented for Scanpy by Davide Cittaro.

Parameters

adata : AnnDataAnnData

The annotated data matrix.

gene_list : Sequence[str]Sequence[str]

The list of gene names used for score calculation.

ctrl_size : intint (default: 50)

Number of reference genes to be sampled from each bin. If len(gene_list) is not too low, you can set ctrl_size=len(gene_list).

gene_pool : Sequence[str] | NoneOptional[Sequence[str]] (default: None)

Genes for sampling the reference set. Default is all genes.

n_bins : intint (default: 25)

Number of expression level bins for sampling.

score_name : strstr (default: 'score')

Name of the field to be added in .obs.

random_state : None | int | RandomStateUnion[None, int, RandomState] (default: 0)

The random seed for sampling.

copy : boolbool (default: False)

Copy adata or modify it inplace.

use_raw : bool | NoneOptional[bool] (default: None)

Whether to use raw attribute of adata. Defaults to True if .raw is present.

Changed in version 1.4.5: Default value changed from False to None.

Return type

AnnData | NoneOptional[AnnData]

Returns

Depending on copy, returns or updates adata with an additional field score_name.

Examples

See this notebook.