scanpy.tl.score_genes

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scanpy.tl.score_genes#

scanpy.tl.score_genes(adata, gene_list, *, ctrl_as_ref=True (sc.settings.preset='scanpy-v1' – changes in 2.0), ctrl_size=50, gene_pool=None, n_bins=25, score_name='score', rng=None, copy=False, use_raw=None, layer=None)[source]#

Score a set of genes [Tirosh et al., 2016].

The score is the average expression of a set of genes after subtraction by 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 [Tirosh et al., 2016] (“MITF and AXL expression programs and cell scores” in materials and methods) and has been implemented for Scanpy by Davide Cittaro.

Array type support#

Array type

supported

… experimentally in dask Array

numpy.ndarray

✅

❌

scipy.sparse.{csr,csc}_{array,matrix}

✅

❌
Parameters:
adata AnnData

The annotated data matrix.

gene_list Sequence[str] | pd.Index[str]

The list of gene names used for score calculation.

ctrl_as_ref bool | Default (default: True (sc.settings.preset='scanpy-v1' – changes in 2.0))

Allow the algorithm to use the control genes as reference. Will be changed to False in scanpy 2.0.

ctrl_size int (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] | pd.Index[str] | None (default: None)

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

n_bins int (default: 25)

Number of expression level bins for sampling.

score_name str (default: 'score')

Name of the field to be added in .obs.

rng SeedLike | RNGLike | None (default: None)

Random number generation to control stochasticity.

If a type:SeedLike value, it’s used to seed a new random number generator; If a numpy.random.Generator, rng’s state will be directly advanced; If None, a non-reproducible random number generator is used. See numpy.random.default_rng() for more details.

The default value matches legacy scanpy behavior and will change to None in scanpy 2.0.

copy bool (default: False)

Copy adata or modify it inplace.

use_raw bool | None (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.

layer str | None (default: None)

Key from adata.layers whose value will be used to perform tests on.

Return type:

AnnData | None

Returns:

Returns None if copy=False, else returns an AnnData object. Sets the following field:

adata.obs[score_name]numpy.ndarray (dtype float)

Scores of each cell.

Examples

See this notebook.

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