stereo.core.StPipeline.filter_cells

StPipeline.filter_cells(min_counts=None, max_counts=None, min_genes=None, max_genes=None, pct_counts_mt=None, cell_list=None, excluded=False, filter_raw=True, use_raw=None, layer=None, inplace=True, **kwargs)[source]

Filter cells based on counts or the numbers of genes expressed.

Parameters:

  • min_counts (Optional[int]) – minimum number of counts required for a cell to pass fitlering.

  • max_counts (Optional[int]) – maximum number of counts required for a cell to pass fitlering.

  • min_genes (Optional[int]) – minimum number of genes expressed required for a cell to pass filtering.

  • max_genes (Optional[int]) – maximum number of genes expressed required for a cell to pass filtering.

  • pct_counts_mt (Optional[float]) – maximum number of pct_counts_mt required for a cell to pass filtering.

  • cell_list (Optional[list]) – the list of cells to be retained.

  • excluded (Optional[bool]) – set it to True to exclude the cells specified by parameter cell_list while False to include.

  • filter_raw (Optional[bool]) – whether to filter raw data meanwhile.

  • use_raw (Optional[bool]) – whether to use raw data to calculate QC indicators, by default, use raw data if it exists.

  • layer (Optional[str]) – the key of layer to be used for calculating QC indicators, if gave, the use_raw will be ignored.

  • inplace (bool) – whether to replace the previous data or return a new data.

Returns:

  • An object of StereoExpData.

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