stereo.core.StPipeline.normalize_total

StPipeline.normalize_total(target_sum=10000, layer=None, inplace=True, add_layer=False, res_key='normalize_total')[source]

Normalize total counts over all genes per cell such that each cell has the same total count after normalization.

Parameters:

  • target_sum (int) – the number of total counts per cell after normalization, if None, each cell has a total count equal to the median of total counts for all cells before normalization.

  • layer (Optional[str]) – the key of layer to be used instead of the data.exp_matrix.

  • inplace (bool) – whether to replace the data.exp_matrix or save the result in data.layers.

  • add_layer (bool) – whether to save the result in data.layers simultaneously when inplace is True.

  • res_key (str) – the key to save the result in data.layers when inplace is False or add_layer is True.

Return type:

Depending on inplace, if True, the data will be replaced by those normalized