revise.config.runner_conf.BenchmarkImputeConf

class revise.config.runner_conf.BenchmarkImputeConf(sample_name: 'str', raw_data_path: 'str', result_root_path: 'str', cell_type_col: 'str', confidence_col: 'str', unknown_key: 'str', st_file: 'str', gt_svc_file: 'str', sc_ref_file: 'str', annotate_mode: 'str', case_subdir: 'Optional[str]' = None, prep_min_cells: 'int' = 30, prep_min_counts: 'int' = 60, annotate_pot_reg: 'float' = 0.01, annotate_pot_reg_m: 'float' = 0.0001, annotate_pot_reg_type: 'str' = 'kl', rec_graph_preprocess: 'bool' = True, rec_graph_n_pcs: 'int' = 50, rec_graph_n_neighbors: 'int' = 15, rec_impute_pot_reg: 'float' = 5.0, rec_impute_pot_reg_m: 'float' = 0.0, rec_impute_pot_reg_type: 'str' = 'kl', rec_merge_subcluster_method: 'str' = 'mean', rec_subcluster_resolution: 'int' = 3, rec_impute_prune_flag: 'bool' = True, rec_impute_n_neighbors: 'int' = 1, rec_impute_method: 'str' = 'mean')[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, gt_svc_file: str, sc_ref_file: str, annotate_mode: str, case_subdir: str | None = None, prep_min_cells: int = 30, prep_min_counts: int = 60, annotate_pot_reg: float = 0.01, annotate_pot_reg_m: float = 0.0001, annotate_pot_reg_type: str = 'kl', rec_graph_preprocess: bool = True, rec_graph_n_pcs: int = 50, rec_graph_n_neighbors: int = 15, rec_impute_pot_reg: float = 5.0, rec_impute_pot_reg_m: float = 0.0, rec_impute_pot_reg_type: str = 'kl', rec_merge_subcluster_method: str = 'mean', rec_subcluster_resolution: int = 3, rec_impute_prune_flag: bool = True, rec_impute_n_neighbors: int = 1, rec_impute_method: str = 'mean') → None

Methods

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

Attributes

`annotate_pot_reg`
`annotate_pot_reg_m`
`annotate_pot_reg_type`
`case_subdir`
`gt_svc_file_path`
`prep_min_cells`
`prep_min_counts`
`rec_graph_n_neighbors`
`rec_graph_n_pcs`
`rec_graph_preprocess`
`rec_impute_method`
`rec_impute_n_neighbors`
`rec_impute_pot_reg`
`rec_impute_pot_reg_m`
`rec_impute_pot_reg_type`
`rec_impute_prune_flag`
`rec_merge_subcluster_method`
`rec_subcluster_resolution`
`result_dir`
`sc_ref_file_path`
`st_file_path`
`st_file`
`gt_svc_file`
`sc_ref_file`
`annotate_mode`
`sample_name`
`raw_data_path`
`result_root_path`
`cell_type_col`
`confidence_col`
`unknown_key`

st_file: str

gt_svc_file: str

sc_ref_file: str

annotate_mode: str

case_subdir: str | None = None

prep_min_cells: int = 30

prep_min_counts: int = 60

annotate_pot_reg: float = 0.01

annotate_pot_reg_m: float = 0.0001

annotate_pot_reg_type: str = 'kl'

rec_graph_preprocess: bool = True

rec_graph_n_pcs: int = 50

rec_graph_n_neighbors: int = 15

rec_impute_pot_reg: float = 5.0

rec_impute_pot_reg_m: float = 0.0

rec_impute_pot_reg_type: str = 'kl'

rec_merge_subcluster_method: str = 'mean'

rec_subcluster_resolution: int = 3

rec_impute_prune_flag: bool = True

rec_impute_n_neighbors: int = 1

rec_impute_method: str = 'mean'

property result_dir

property st_file_path

property sc_ref_file_path

property gt_svc_file_path