alphapepttools.metrics.number_detected

alphapepttools.metrics.number_detected#

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

Count the number of detected features per observation or detected observations 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 count. - “obs” (default): Count detected features per observation.

    Result is added to adata.obs.

    • ”var”: Count detected observations per feature. Result is added to adata.var.

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

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