mmc.run_threshold()

mmochi.thresholding.run_threshold(markname, adata, data_key, thresh)

Lightweight wrapper to find the marker (utils.get_data()), then performs pos/neg/? thresholding on all events in the AnnData, given a list of positive and negative thresholds.

Parameters:

  • markname (str) – Name of the marker to threshold

  • adata (AnnData) – AnnData object containing normalized (and possibly batch corrected) events for thresholding

  • data_key (Union[str, list, None]) – Name of the key(s) in .obsm[] or .var[MODALITY_COLUMN] to look for when searching for markname

  • thresh (Sequence[Union[int, float]]) – Upper and lower thresholds to apply for positive and negative populations (no specific order needed)

Returns:

1D array that is the length of the adata, with “pos” if data is >= to the upper threshold, “neg” if <= lower threshold, and “?” if in between upper and lower

Return type:

np.array