stereo.core.StPipeline.normalize_total

StPipeline.normalize_total(target_sum=10000, inplace=True, 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.

  • inplace (bool) – whether to inplcae previous data or get a new express matrix after normalize_total.

  • res_key (str) – the key to get targeted result from self.result.

Returns:

  • An object of StereoExpData.

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