visionpy.signatures_from_gmt#

visionpy.signatures_from_gmt(gmt_files, adata, use_raw=False)[source]#

Compute signature scores from .gmt files.

Parameters:

  • gmt_files (Sequence[str]) – List of .gmt files to use for signature computation.

  • adata (AnnData) – AnnData object to compute signatures for.

  • use_raw (bool (default: False)) – Whether to use adata.raw.X for signature computation.

  • layer – Layer to use for signature computation. Only used if use_raw is False.

  • scale – Whether to scale the signature scores (using VISION-style correction). Not used if use_decoupler is True.

  • use_decoupler – Use decouplerpy wmean for computing signature scores. Otherwise, closed-form VISION computation is performed.

Return type:

DataFrame

Returns:

Genes by signatures dataframe and cells by signatures dataframe with scores. Index is aligned to genes from adata.