Analysis

benchmark_directory(results_dir_and_input, score_order, output_prefix, threshold, gene_analysis, variant_analysis, disease_analysis, plot_type)

Benchmark prioritisation performance for a single run.

Parameters:

Name	Type	Description	Default
results_dir_and_input	TrackInputOutputDirectories	Input and output directories for tracking results.	required
score_order	str	The order in which scores are arranged, this can be either ascending or descending.	required
output_prefix	str	Prefix for the benchmark output file names.	required
threshold	float	The threshold for benchmark evaluation.	required
gene_analysis	bool	Boolean flag indicating whether to benchmark gene results.	required
variant_analysis	bool	Boolean flag indicating whether to benchmark variant results.	required
disease_analysis	bool	Boolean flag indicating whether to benchmark disease results.	required
plot_type	str	Type of plot for benchmark visualisation.	required

Source code in src/pheval/analyse/analysis.py

def benchmark_directory(
    results_dir_and_input: TrackInputOutputDirectories,
    score_order: str,
    output_prefix: str,
    threshold: float,
    gene_analysis: bool,
    variant_analysis: bool,
    disease_analysis: bool,
    plot_type: str,
) -> None:
    """
    Benchmark prioritisation performance for a single run.

    Args:
        results_dir_and_input (TrackInputOutputDirectories): Input and output directories for tracking results.
        score_order (str): The order in which scores are arranged, this can be either ascending or descending.
        output_prefix (str): Prefix for the benchmark output file names.
        threshold (float): The threshold for benchmark evaluation.
        gene_analysis (bool): Boolean flag indicating whether to benchmark gene results.
        variant_analysis (bool): Boolean flag indicating whether to benchmark variant results.
        disease_analysis (bool): Boolean flag indicating whether to benchmark disease results.
        plot_type (str): Type of plot for benchmark visualisation.
    """
    if gene_analysis:
        _run_benchmark(
            results_dir_and_input=results_dir_and_input,
            score_order=score_order,
            output_prefix=output_prefix,
            threshold=threshold,
            plot_type=plot_type,
            benchmark_generator=GeneBenchmarkRunOutputGenerator(),
        )
    if variant_analysis:
        _run_benchmark(
            results_dir_and_input=results_dir_and_input,
            score_order=score_order,
            output_prefix=output_prefix,
            threshold=threshold,
            plot_type=plot_type,
            benchmark_generator=VariantBenchmarkRunOutputGenerator(),
        )
    if disease_analysis:
        _run_benchmark(
            results_dir_and_input=results_dir_and_input,
            score_order=score_order,
            output_prefix=output_prefix,
            threshold=threshold,
            plot_type=plot_type,
            benchmark_generator=DiseaseBenchmarkRunOutputGenerator(),
        )

benchmark_run_comparisons(results_directories, score_order, output_prefix, threshold, gene_analysis, variant_analysis, disease_analysis, plot_type)

Benchmark prioritisation performance for several runs.

Parameters:

Name	Type	Description	Default
results_directories	List[TrackInputOutputDirectories]	Input and output directories for tracking results.	required
score_order	str	The order in which scores are arranged, this can be either ascending or descending.	required
output_prefix	str	Prefix for the benchmark output file names.	required
threshold	float	The threshold for benchmark evaluation.	required
gene_analysis	bool	Boolean flag indicating whether to benchmark gene results.	required
variant_analysis	bool	Boolean flag indicating whether to benchmark variant results.	required
disease_analysis	bool	Boolean flag indicating whether to benchmark disease results.	required
plot_type	str	Type of plot for benchmark visualisation.	required

Source code in src/pheval/analyse/analysis.py

def benchmark_run_comparisons(
    results_directories: List[TrackInputOutputDirectories],
    score_order: str,
    output_prefix: str,
    threshold: float,
    gene_analysis: bool,
    variant_analysis: bool,
    disease_analysis: bool,
    plot_type: str,
) -> None:
    """
    Benchmark prioritisation performance for several runs.

    Args:
        results_directories (List[TrackInputOutputDirectories]): Input and output directories for tracking results.
        score_order (str): The order in which scores are arranged, this can be either ascending or descending.
        output_prefix (str): Prefix for the benchmark output file names.
        threshold (float): The threshold for benchmark evaluation.
        gene_analysis (bool): Boolean flag indicating whether to benchmark gene results.
        variant_analysis (bool): Boolean flag indicating whether to benchmark variant results.
        disease_analysis (bool): Boolean flag indicating whether to benchmark disease results.
        plot_type (str): Type of plot for benchmark visualisation.
    """
    if gene_analysis:
        _run_benchmark_comparison(
            results_directories=results_directories,
            score_order=score_order,
            output_prefix=output_prefix,
            threshold=threshold,
            plot_type=plot_type,
            benchmark_generator=GeneBenchmarkRunOutputGenerator(),
        )
    if variant_analysis:
        _run_benchmark_comparison(
            results_directories=results_directories,
            score_order=score_order,
            output_prefix=output_prefix,
            threshold=threshold,
            plot_type=plot_type,
            benchmark_generator=VariantBenchmarkRunOutputGenerator(),
        )
    if disease_analysis:
        _run_benchmark_comparison(
            results_directories=results_directories,
            score_order=score_order,
            output_prefix=output_prefix,
            threshold=threshold,
            plot_type=plot_type,
            benchmark_generator=DiseaseBenchmarkRunOutputGenerator(),
        )