revise.config.runner_conf.ApplicationSpConf

class revise.config.runner_conf.ApplicationSpConf(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', annotate_pot_reg: 'float' = 0.1, annotate_pot_reg_m: 'float' = 0.0, annotate_pot_reg_type: 'str' = 'entropy', prep_st_min_counts: 'int' = 20, prep_st_min_cells: 'int' = 30, prep_sc_min_counts: 'int' = 20, prep_sc_min_cells: 'int' = 50, plot_flag: 'bool' = True, plot_cluster_resolution: 'list' = <factory>, plot_min_genes: 'int' = 20, plot_min_cells: 'int' = 3, plot_sample_size: 'int' = 10000, rec_graph_n_neighbors: 'int' = 10, rec_graph_exp_neighbor_num: 'int' = 10, rec_graph_spatial_neighbor_num: 'int' = 10, rec_graph_method: 'str' = 'joint', rec_graph_alpha: 'float' = 0.4, rec_pot_reg: 'float' = 0.05, rec_pot_reg_m: 'float' = 1.0, rec_pot_reg_type: 'str' = 'kl')[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, annotate_pot_reg: float = 0.1, annotate_pot_reg_m: float = 0.0, annotate_pot_reg_type: str = 'entropy', prep_st_min_counts: int = 20, prep_st_min_cells: int = 30, prep_sc_min_counts: int = 20, prep_sc_min_cells: int = 50, plot_flag: bool = True, plot_cluster_resolution: list = <factory>, plot_min_genes: int = 20, plot_min_cells: int = 3, plot_sample_size: int = 10000, rec_graph_n_neighbors: int = 10, rec_graph_exp_neighbor_num: int = 10, rec_graph_spatial_neighbor_num: int = 10, rec_graph_method: str = 'joint', rec_graph_alpha: float = 0.4, rec_pot_reg: float = 0.05, rec_pot_reg_m: float = 1.0, rec_pot_reg_type: str = 'kl') → None

Methods

__init__(sample_name, raw_data_path, ...)

Attributes

`annotate_pot_reg`
`annotate_pot_reg_m`
`annotate_pot_reg_type`
`plot_flag`
`plot_min_cells`
`plot_min_genes`
`plot_sample_size`
`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_pot_reg`
`rec_pot_reg_m`
`rec_pot_reg_type`
`result_dir`
`sc_ref_file_path`
`st_file_path`
`st_file`
`sc_ref_file`
`annotate_mode`
`plot_cluster_resolution`
`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

annotate_pot_reg: float = 0.1

annotate_pot_reg_m: float = 0.0

annotate_pot_reg_type: str = 'entropy'

prep_st_min_counts: int = 20

prep_st_min_cells: int = 30

prep_sc_min_counts: int = 20

prep_sc_min_cells: int = 50

plot_flag: bool = True

plot_cluster_resolution: list

plot_min_genes: int = 20

plot_min_cells: int = 3

plot_sample_size: int = 10000

rec_graph_n_neighbors: int = 10

rec_graph_exp_neighbor_num: int = 10

rec_graph_spatial_neighbor_num: int = 10

rec_graph_method: str = 'joint'

rec_graph_alpha: float = 0.4

rec_pot_reg: float = 0.05

rec_pot_reg_m: float = 1.0

rec_pot_reg_type: str = 'kl'

rec_alpha = 0.5

property result_dir

property st_file_path

property sc_ref_file_path