alphapepttools.metrics.fraction_complete

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

Calculate the fraction of detected values per observation or per feature.

A value is considered detected if it is not a special value (NaN, zero, negative, or infinite).

Parameters:

• adata (AnnData) – AnnData object

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

• axis (str (default: 'obs')) –

  Axis along which to calculate the fraction. - “obs” (default): Calculate fraction of detected features per observation.

  Result is added to adata.obs.

  • ”var”: Calculate fraction of detected observations per feature. Result is added to adata.var.

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

• 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 fraction values as an array. If inplace is True, modifies adata inplace and returns None.