alphapepttools.metrics.total_intensity

alphapepttools.metrics.total_intensity(adata, *, layer=None, axis='obs', features=None, column='total_intensity', inplace=True)

Calculate sum of intensity per observation or per feature.

Parameters:

• adata (AnnData) – AnnData object

• layer (str | None (default: None)) – Name of the layer to compute the sum on. If None (default), the data matrix X is used.

• axis (str (default: 'obs')) –

  Axis along which to calculate the sum. - “obs” (default): Calculate total intensity per observation.

  Result is added to adata.obs if inplace=True.

  • ”var”: Calculate total intensity per feature. Result is added to adata.var if inplace=True.

• features (list[str] | None (default: None)) – Optional list of specific features (var_names) to include in the sum. If None (default), all features are used. Valid only when axis="obs".

• column (str (default: 'total_intensity')) – Name of the column to add. Default is “total_intensity”.

• inplace (bool (default: True)) – If True (default), modifies adata inplace and adds the result to adata.obs or adata.var. If False, returns the calculated values without modifying adata.

Return type:

ndarray | None

Returns:

np.ndarray | None If inplace is False, returns the sum values as an array. If inplace is True, modifies adata inplace and returns None.