stereo.algorithm.spa_track.SpaTrack.filter_genes

SpaTrack.filter_genes(min_exp_prop_in_genes, n_hvg=2000, focused_cell_types=None)[source]

Filter genes based on the proportion of cells expressing the gene and the highly variable genes.

Only running on the subset of cells that are the neighbors of the LAP.

Parameters:

  • min_exp_prop_in_genes (float) – The minimum proportion of cells expressing the gene, defaults to 0.1

  • n_hvg (int) – The number of highly variable genes to be calculated, defaults to 2000

  • focused_cell_types (Union[list, ndarray, str, None]) – The cell types to be focused on, by default, all cell types will be used.

Returns:

the object of data with filtered genes