stereo.core.StPipeline.filter_cells#
- StPipeline.filter_cells(min_gene=None, max_gene=None, min_n_genes_by_counts=None, max_n_genes_by_counts=None, pct_counts_mt=None, cell_list=None, filter_raw=True, inplace=True)[source]#
Filter cells based on counts or the numbers of genes expressed.
- Parameters:
min_gene (
Optional
[int
]) – minimum number of counts required for a cell to pass fitlering.max_gene (
Optional
[int
]) – maximum number of counts required for a cell to pass fitlering.min_n_genes_by_counts (
Optional
[int
]) – minimum number of genes expressed required for a cell to pass filtering.max_n_genes_by_counts (
Optional
[int
]) – maximum number of genes expressed required for a cell to pass filtering.pct_counts_mt (
Optional
[float
]) – maximum number ofpct_counts_mt
required for a cell to pass filtering.cell_list (
Optional
[list
]) – the list of cells to be retained.filter_raw (
Optional
[bool
]) – whether to filter raw data meanwhile.inplace (
bool
) – whether to inplace the previous data or return a new data.
- Returns:
An object of StereoExpData.
Depending on
inplace
, ifTrue
, the data will be replaced by those filtered.