mmc.update_peak_overrides()

mmochi.landmarking.update_peak_overrides(batch, marker, update_lower, update_upper, peak_overrides={}, current_peaks=None)

Update peak overrides object for a single batch, marker. Can load it from a JSON if provided a string. To use update_upper and update_lower = False, must provide current_peaks dict (often found in adata.uns)

Parameters:

  • batch (str) – The ID corresponding with the batch of interest

  • marker (str) – The name of the marker to edit overrides on

  • update_lower (Union[float, bool, None]) –

  • update_upper (Union[float, bool, None]) – If update_lower or update_upper is False, keep current value for lower or upper, respectively. Otherwise, if they are floats, update to that value. If update_lower is None, then put None as the lower peak, forcing a single positive. If update_upper is None, then put lower as the only item in the override, forcing a single negative.

Return type:

dict

Returns:

peak_overrides: dict

updated peaks_overrides, which can be passed into update_landmark_register, or saved to JSON using save_peak_overrides