mmc.update_landmark_register()

mmochi.landmarking.update_landmark_register(adata, batch, marker, override={}, batch_key=utils.BATCH_KEY, data_key='protein', key_added='landmark_protein', show=False, single_peaks=[], bandwidth=0.2, inclusion_mask=None, **kwargs)

Landmark registration batch correction for ADT expression for a single marker on a single batch. landmark_register_adts() must be run before this. See landmark_register_adts for more details.

Parameters:

  • adata (AnnData) – object with [batch_key] in .obs, [data_key] log or arcsine normalized data in .obsm to be batch corrected

  • batch (str) – Batch to in .obs[batch_key] to define batch to landmark register

  • marker (str) – Corresponding marker of interest

  • override (Union[List[float], dict, str] (default: {})) – Can be a listlike of two floats corresponding to the positive and negative peaks, or a dict with an item in { batch:{marker:[0.1,0.5]} }. To force a positive peak, pass [None,float] as the override. To force a negative peak, you can pass simply [float]. Can also be passed as a str, corresponding to the file path of a JSON saved with this dict format.

  • batch_key (str (default: utils.BATCH_KEY)) – column in the .obs of the adata, corresponding to batch information

  • data_key (str (default: 'protein')) – key of the DataFrame in the .obsm of the adata, corresponding to the ADT expression information

  • key_added (str (default: 'landmark_protein')) – key of the DataFrame in the .obsm of the adata to insert landmark registered ADT expression

  • show (Union[bool, int] (default: False)) – Whether to show plotted intermediates to better reveal peak detection. Note, this disables parallel processing. Integers (up to 3) correspond to increased verbosity level.

  • single_peaks (Union[bool, List[str]] (default: [])) – Columns in adata.obsm[data_key] corresponding to ADTs to only align a single peak of. Can also just be True or False.

  • marker_bandwidths – In the format {marker:0.5}, to override bandwidths used for individual markers, or just a bandwidth number to use that.

  • inclusion_mask (Union[str, List, None] (default: None)) – Mask of events included in landmark registration warping calculation or a column in the .obs with such a mask

  • **kwargs – Other key word arguments are passed to _detect_landmarks

Return type:

Adata with batch corrected [data_key] over batch_key