bioalpha.singlecell.read_gene_signatures

bioalpha.singlecell.read_gene_signatures(json_file: Path, adata: AnnData | H5ADMap | None = None, key_added: str | None = None, key_name: str | None = 'systematicName', key_gene: str | None = 'geneSymbols', copy: bool = False) → List[GeneSignature] | AnnData | None

Read gene signatures from JSON file.

Parameters:

  • json_file (Path) – path to gene signatures file.

  • adata (Optional[AnnData], default = None) – The annotated data matrix of shape n_obs x n_vars. If passed a not None value, gene_signatures will be saved in adata.uns. Otherwise, return a list gene signatures.

  • key_added (Optional[str], default = None) – The key in adata.uns information is saved to. Can not be set when adata is None.

  • key_name (Optional[str], default = "systematicName",) – The key for loadding the name of gene set. (See the below example).

  • key_gene (Optional[str], default = "geneSymbols") – The key for loadding the gene_signatures. (See the below example).

  • copy (bool, default = False) – Whether to copy adata or modify it inplace.

Returns:

  • If adata is passed, "gene_sigs" will be added in

  • adata.uns and returned if copy = True.

  • Otherwise, return a List[GeneSignature].

Example

>>> # Download gene sets here
... # https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2023.1.Mm/
>>> from bioalpha import sc
>>> sc.read_gene_signatures("m5.go.v2023.1.Mm.json")
[GeneSignature(name='MM5283', gene2weight=frozendict.frozendict({'Aasdhppt': 1,  'Aldh1l1': 1, 'Aldh1l2': 1, 'Mthfd1': 1, 'Mthfd1l': 1, 'Mthfd2l': 1})),...]
>>> # change the key_name will change the GeneSignature name
>>> sc.read_gene_signatures("m5.go.v2023.1.Mm.json", key_name="exactSource")
[GeneSignature(name='GO:0009256', gene2weight=frozendict.frozendict({'Aasdhppt': 1,   'Aldh1l1': 1, 'Aldh1l2': 1, 'Mthfd1': 1, 'Mthfd1l': 1, 'Mthfd2l': 1})),...]
>>> # NOTE: when file structures like this
... {
  gene_set1: ["gene1", "gene2"],
  gene_set2: ["gene1", "gene2"],
  ...
}
... # key_name and key_gene must be set to None