pegasus.calc_signature_score

pegasus.calc_signature_score(data, signatures, n_bins=50)[source]

Calculate signature / gene module score.

This is an improved version of Livnat et al. 2018 Cell implementation.

Parameters

  • data (anndata.AnnData) – Annotated data matrix with rows for cells and columns for genes.

  • signatures (Dict[str, List[str]]) – A dictionary containing multiple signature score calculation requests. Each score will be stored in data.obs field with key as the keyword. The value of the dict is a list of gene symbols.

  • n_bins (int, optional, default: 50) –

Return type

None

Returns

  • None.

  • Update data.obs –

    • data.obs["key"]: signature / gene module score for signature “key”

  • Update data.var –

    • data.var["mean"]: Mean expression of each gene across all cells. Only updated if “mean” does not exist in data.var.

    • data.var["bins"]: Bin category for each gene. Only updated if data.uns[“sig_n_bins”] is updated.

  • Update data.obsm –

    • data.obsm["sig_background"]: Expected signature score for each bin category. Only updated if data.uns[“sig_n_bins”] is updated.

  • Update data.uns –

    • data.uns["sig_n_bins"]: Number of bins to partition genes into. Only updated if “sig_n_bins” does not exist or the recorded number of bins does not match n_bins.

Examples

>>> pg.calc_signature_score(data, {"T_cell_sig": ["CD3D", "CD3E", "CD3G", "TRAC"]})