immuneML.workflows.instructions.clustering package

Submodules

immuneML.workflows.instructions.clustering.ClusteringInstruction module

immuneML.workflows.instructions.clustering.ClusteringReportHandler module

class immuneML.workflows.instructions.clustering.ClusteringReportHandler.ClusteringReportHandler(reports: List[Report])

Bases: object

Manages report generation for clustering results.

run_clustering_reports(state: ClusteringState)

Generate overall clustering reports.

run_item_reports(cl_item: ClusteringItem, analysis_desc: str, run_id: int, path: Path, state: ClusteringState) → list

Generate reports for individual clustering items.

immuneML.workflows.instructions.clustering.ClusteringRunner module

immuneML.workflows.instructions.clustering.ClusteringState module

class immuneML.workflows.instructions.clustering.ClusteringState.ClusteringConfig(name: str, dataset: immuneML.data_model.datasets.Dataset.Dataset, metrics: List[str], split_config: immuneML.hyperparameter_optimization.config.SplitConfig.SplitConfig, validation_type: List[str], clustering_settings: List[immuneML.workflows.instructions.clustering.clustering_run_model.ClusteringSetting], region_type: immuneML.data_model.SequenceParams.RegionType = <RegionType.IMGT_CDR3: 'cdr3'>, label_config: immuneML.environment.LabelConfiguration.LabelConfiguration = None, sequence_type: immuneML.environment.SequenceType.SequenceType = <SequenceType.AMINO_ACID: 'sequence_aa'>)

Bases: object

clustering_settings: List[ClusteringSetting]

dataset: Dataset

label_config: LabelConfiguration = None

metrics: List[str]

name: str

region_type: RegionType = 'cdr3'

sequence_type: SequenceType = 'sequence_aa'

split_config: SplitConfig

validation_type: List[str]

class immuneML.workflows.instructions.clustering.ClusteringState.ClusteringItemResult(item: immuneML.workflows.instructions.clustering.clustering_run_model.ClusteringItem, report_results: List[immuneML.reports.ReportResult.ReportResult] = <factory>)

Bases: object

item: ClusteringItem

report_results: List[ReportResult]

class immuneML.workflows.instructions.clustering.ClusteringState.ClusteringResultPerRun(run_id: int, run_type: str, items: Dict[str, immuneML.workflows.instructions.clustering.ClusteringState.ClusteringItemResult] = <factory>)

Bases: object

get_cl_item(cl_setting: str | ClusteringSetting)

items: Dict[str, ClusteringItemResult]

run_id: int

run_type: str

class immuneML.workflows.instructions.clustering.ClusteringState.ClusteringResults(discovery: immuneML.workflows.instructions.clustering.ClusteringState.ClusteringResultPerRun = None, method_based_validation: immuneML.workflows.instructions.clustering.ClusteringState.ClusteringResultPerRun = None, result_based_validation: immuneML.workflows.instructions.clustering.ClusteringState.ClusteringResultPerRun = None)

Bases: object

discovery: ClusteringResultPerRun = None

method_based_validation: ClusteringResultPerRun = None

result_based_validation: ClusteringResultPerRun = None

class immuneML.workflows.instructions.clustering.ClusteringState.ClusteringState(name: str, config: immuneML.workflows.instructions.clustering.ClusteringState.ClusteringConfig, result_path: pathlib.Path = None, clustering_items: List[immuneML.workflows.instructions.clustering.ClusteringState.ClusteringResults] = <factory>, predictions_paths: List[Dict[str, pathlib.Path]] = None, discovery_datasets: List[immuneML.data_model.datasets.Dataset.Dataset] = None, validation_datasets: List[immuneML.data_model.datasets.Dataset.Dataset] = None, clustering_report_results: List[immuneML.reports.ReportResult.ReportResult] = <factory>)

Bases: object

add_cl_result_per_run(run_id: int, analysis_desc: str, cl_item_result: ClusteringResultPerRun)

clustering_items: List[ClusteringResults]

clustering_report_results: List[ReportResult]

config: ClusteringConfig

discovery_datasets: List[Dataset] = None

name: str

predictions_paths: List[Dict[str, Path]] = None

result_path: Path = None

validation_datasets: List[Dataset] = None

immuneML.workflows.instructions.clustering.ValidationHandler module

immuneML.workflows.instructions.clustering.clustering_run_model module

class immuneML.workflows.instructions.clustering.clustering_run_model.ClusteringItem(dataset: immuneML.data_model.datasets.Dataset.Dataset = None, method: immuneML.ml_methods.clustering.ClusteringMethod.ClusteringMethod = None, encoder: immuneML.encodings.DatasetEncoder.DatasetEncoder = None, internal_performance: immuneML.workflows.instructions.clustering.clustering_run_model.DataFrameWrapper = None, external_performance: immuneML.workflows.instructions.clustering.clustering_run_model.DataFrameWrapper = None, predictions: numpy.ndarray = None, cl_setting: immuneML.workflows.instructions.clustering.clustering_run_model.ClusteringSetting = None)

Bases: object

cl_setting: ClusteringSetting = None

dataset: Dataset = None

encoder: DatasetEncoder = None

external_performance: DataFrameWrapper = None

internal_performance: DataFrameWrapper = None

method: ClusteringMethod = None

predictions: ndarray = None

class immuneML.workflows.instructions.clustering.clustering_run_model.ClusteringSetting(encoder: immuneML.encodings.DatasetEncoder.DatasetEncoder, encoder_params: dict, encoder_name: str, clustering_method: immuneML.ml_methods.clustering.ClusteringMethod.ClusteringMethod, clustering_params: dict, clustering_method_name: str, dim_reduction_method: immuneML.ml_methods.dim_reduction.DimRedMethod.DimRedMethod = None, dim_red_params: dict = None, dim_red_name: str = None, path: pathlib.Path = None)

Bases: object

clustering_method: ClusteringMethod

clustering_method_name: str

clustering_params: dict

dim_red_name: str = None

dim_red_params: dict = None

dim_reduction_method: DimRedMethod = None

encoder: DatasetEncoder

encoder_name: str

encoder_params: dict

get_key() → str

path: Path = None

class immuneML.workflows.instructions.clustering.clustering_run_model.DataFrameWrapper(path: Path, df: pandas.DataFrame = None)

Bases: object

get_df()

Module contents