revise.config.runner_conf.ApplicationScConf

class revise.config.runner_conf.ApplicationScConf(sample_name: 'str', raw_data_path: 'str', result_root_path: 'str', cell_type_col: 'str', confidence_col: 'str', unknown_key: 'str', st_file: 'str', sc_ref_file: 'str', annotate_mode: 'Optional[str]' = None, annotate_pot_reg: 'float' = 0.06, annotate_pot_reg_m: 'float' = 0.015, annotate_pot_reg_type: 'str' = 'entropy', prep_st_min_counts: 'int' = 60, prep_st_min_cells: 'int' = 100, prep_sc_min_counts: 'int' = 0, prep_sc_min_cells: 'int' = 100, rec_graph_n_neighbors: 'int' = 10, rec_graph_exp_neighbor_num: 'int' = 15, rec_graph_spatial_neighbor_num: 'int' = 6, rec_graph_method: 'str' = 'joint', rec_graph_alpha: 'float' = 0.2, rec_pot_reg: 'float' = 0.06, rec_pot_reg_m: 'float' = 0.015, rec_pot_reg_type: 'str' = 'entropy', rec_match_spot_sum: 'bool' = False)[source]

Bases: BaseConf

__init__(sample_name: str, raw_data_path: str, result_root_path: str, cell_type_col: str, confidence_col: str, unknown_key: str, st_file: str, sc_ref_file: str, annotate_mode: str | None = None, annotate_pot_reg: float = 0.06, annotate_pot_reg_m: float = 0.015, annotate_pot_reg_type: str = 'entropy', prep_st_min_counts: int = 60, prep_st_min_cells: int = 100, prep_sc_min_counts: int = 0, prep_sc_min_cells: int = 100, rec_graph_n_neighbors: int = 10, rec_graph_exp_neighbor_num: int = 15, rec_graph_spatial_neighbor_num: int = 6, rec_graph_method: str = 'joint', rec_graph_alpha: float = 0.2, rec_pot_reg: float = 0.06, rec_pot_reg_m: float = 0.015, rec_pot_reg_type: str = 'entropy', rec_match_spot_sum: bool = False) → None

Methods

__init__(sample_name, raw_data_path, ...[, ...])

Attributes

`annotate_mode`
`annotate_pot_reg`
`annotate_pot_reg_m`
`annotate_pot_reg_type`
`prep_sc_min_cells`
`prep_sc_min_counts`
`prep_st_min_cells`
`prep_st_min_counts`
`rec_alpha`
`rec_graph_alpha`
`rec_graph_exp_neighbor_num`
`rec_graph_method`
`rec_graph_n_neighbors`
`rec_graph_spatial_neighbor_num`
`rec_match_spot_sum`
`rec_pot_reg`
`rec_pot_reg_m`
`rec_pot_reg_type`
`result_dir`
`sc_ref_file_path`
`st_file_path`
`st_file`
`sc_ref_file`
`sample_name`
`raw_data_path`
`result_root_path`
`cell_type_col`
`confidence_col`
`unknown_key`

st_file: str

sc_ref_file: str

annotate_mode: str | None = None

annotate_pot_reg: float = 0.06

annotate_pot_reg_m: float = 0.015

annotate_pot_reg_type: str = 'entropy'

prep_st_min_counts: int = 60

prep_st_min_cells: int = 100

prep_sc_min_counts: int = 0

prep_sc_min_cells: int = 100

rec_graph_n_neighbors: int = 10

rec_graph_exp_neighbor_num: int = 15

rec_graph_spatial_neighbor_num: int = 6

rec_graph_method: str = 'joint'

rec_graph_alpha: float = 0.2

rec_pot_reg: float = 0.06

rec_pot_reg_m: float = 0.015

rec_pot_reg_type: str = 'entropy'

rec_alpha = 0.5

rec_match_spot_sum: bool = False

property result_dir

property st_file_path

property sc_ref_file_path