revise.config.runner_conf.BenchmarkSrConf

class revise.config.runner_conf.BenchmarkSrConf(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', spot_size: 'int', annotate_mode: 'str', case_subdir: 'Optional[str]' = None, annotate_pot_reg: 'float' = 0.01, annotate_pot_reg_m: 'float' = 0.0001, annotate_pot_reg_type: 'str' = 'kl', svc_completeness: 'bool' = True, rec_graph_n_neighbors: 'int' = 20, rec_graph_exp_neighbor_num: 'int' = 10, rec_graph_spatial_neighbor_num: 'int' = 20, rec_graph_method: 'str' = 'joint', rec_graph_alpha: 'float' = 0.2, rec_pot_reg: 'float' = 0.05, rec_pot_reg_m: 'float' = 1.0, rec_pot_reg_type: 'str' = 'kl', rec_alpha: 'float' = 1.0, rec_graph_agg_enabled: 'bool' = False, sr_noise_enabled: 'bool' = False, sr_noise_lambda: 'float' = 0.0, sr_noise_k: 'int' = 4, sr_noise_weight: 'str' = 'distance', sr_noise_preserve_total_counts: 'bool' = True, sr_noise_seed: 'int' = 42)[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, spot_size: int, annotate_mode: str, case_subdir: str | None = None, annotate_pot_reg: float = 0.01, annotate_pot_reg_m: float = 0.0001, annotate_pot_reg_type: str = 'kl', svc_completeness: bool = True, rec_graph_n_neighbors: int = 20, rec_graph_exp_neighbor_num: int = 10, rec_graph_spatial_neighbor_num: int = 20, rec_graph_method: str = 'joint', rec_graph_alpha: float = 0.2, rec_pot_reg: float = 0.05, rec_pot_reg_m: float = 1.0, rec_pot_reg_type: str = 'kl', rec_alpha: float = 1.0, rec_graph_agg_enabled: bool = False, sr_noise_enabled: bool = False, sr_noise_lambda: float = 0.0, sr_noise_k: int = 4, sr_noise_weight: str = 'distance', sr_noise_preserve_total_counts: bool = True, sr_noise_seed: int = 42) → 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`
`pm_on_cell_file`
`rec_alpha`
`rec_graph_agg_enabled`
`rec_graph_alpha`
`rec_graph_exp_neighbor_num`
`rec_graph_method`
`rec_graph_n_neighbors`
`rec_graph_spatial_neighbor_num`
`rec_pot_reg`
`rec_pot_reg_m`
`rec_pot_reg_type`
`result_dir`
`sc_ref_file_path`
`sr_noise_enabled`
`sr_noise_k`
`sr_noise_lambda`
`sr_noise_preserve_total_counts`
`sr_noise_seed`
`sr_noise_weight`
`st_file_path`
`svc_completeness`
`st_file`
`gt_svc_file`
`sc_ref_file`
`spot_size`
`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

spot_size: int

annotate_mode: str

case_subdir: str | None = None

annotate_pot_reg: float = 0.01

annotate_pot_reg_m: float = 0.0001

annotate_pot_reg_type: str = 'kl'

svc_completeness: bool = True

rec_graph_n_neighbors: int = 20

rec_graph_exp_neighbor_num: int = 10

rec_graph_spatial_neighbor_num: int = 20

rec_graph_method: str = 'joint'

rec_graph_alpha: float = 0.2

rec_pot_reg: float = 0.05

rec_pot_reg_m: float = 1.0

rec_pot_reg_type: str = 'kl'

rec_alpha: float = 1.0

rec_graph_agg_enabled: bool = False

sr_noise_enabled: bool = False

sr_noise_lambda: float = 0.0

sr_noise_k: int = 4

sr_noise_weight: str = 'distance'

sr_noise_preserve_total_counts: bool = True

sr_noise_seed: int = 42

property result_dir

property st_file_path

property gt_svc_file_path

property sc_ref_file_path

property pm_on_cell_file