risk-network 0.0.11__py3-none-any.whl → 0.0.12b0__py3-none-any.whl

risk/stats/stat_tests.py

@@ -1,267 +0,0 @@
-"""
-risk/stats/stat_tests
-~~~~~~~~~~~~~~~~~~~~~
-"""
-
-from typing import Any, Dict
-
-import numpy as np
-from scipy.sparse import csr_matrix
-from scipy.stats import binom
-from scipy.stats import chi2
-from scipy.stats import hypergeom
-from scipy.stats import norm
-from scipy.stats import poisson
-
-
-def compute_binom_test(
-    neighborhoods: csr_matrix,
-    annotations: csr_matrix,
-    null_distribution: str = "network",
-) -> Dict[str, Any]:
-    """Compute Binomial test for enrichment and depletion in neighborhoods with selectable null distribution.
-
-    Args:
-        neighborhoods (csr_matrix): Sparse binary matrix representing neighborhoods.
-        annotations (csr_matrix): Sparse binary matrix representing annotations.
-        null_distribution (str, optional): Type of null distribution ('network' or 'annotations'). Defaults to "network".
-
-    Returns:
-        Dict[str, Any]: Dictionary containing depletion and enrichment p-values.
-    """
-    # Get the total number of nodes in the network
-    total_nodes = neighborhoods.shape[1]
-
-    # Compute sums (remain sparse here)
-    neighborhood_sizes = neighborhoods.sum(axis=1)  # Row sums
-    annotation_totals = annotations.sum(axis=0)  # Column sums
-    # Compute probabilities (convert to dense)
-    if null_distribution == "network":
-        p_values = (annotation_totals / total_nodes).A.flatten()  # Dense 1D array
-    elif null_distribution == "annotations":
-        p_values = (annotation_totals / annotations.sum()).A.flatten()  # Dense 1D array
-    else:
-        raise ValueError(
-            "Invalid null_distribution value. Choose either 'network' or 'annotations'."
-        )
-
-    # Observed counts (sparse matrix multiplication)
-    annotated_counts = neighborhoods @ annotations  # Sparse result
-    annotated_counts_dense = annotated_counts.toarray()  # Convert for dense operations
-
-    # Compute enrichment and depletion p-values
-    enrichment_pvals = 1 - binom.cdf(annotated_counts_dense - 1, neighborhood_sizes.A, p_values)
-    depletion_pvals = binom.cdf(annotated_counts_dense, neighborhood_sizes.A, p_values)
-
-    return {"enrichment_pvals": enrichment_pvals, "depletion_pvals": depletion_pvals}
-
-
-def compute_chi2_test(
-    neighborhoods: csr_matrix,
-    annotations: csr_matrix,
-    null_distribution: str = "network",
-) -> Dict[str, Any]:
-    """Compute chi-squared test for enrichment and depletion in neighborhoods with selectable null distribution.
-
-    Args:
-        neighborhoods (csr_matrix): Sparse binary matrix representing neighborhoods.
-        annotations (csr_matrix): Sparse binary matrix representing annotations.
-        null_distribution (str, optional): Type of null distribution ('network' or 'annotations'). Defaults to "network".
-
-    Returns:
-        Dict[str, Any]: Dictionary containing depletion and enrichment p-values.
-    """
-    # Total number of nodes in the network
-    total_node_count = neighborhoods.shape[0]
-
-    if null_distribution == "network":
-        # Case 1: Use all nodes as the background
-        background_population = total_node_count
-        neighborhood_sums = neighborhoods.sum(axis=0)  # Column sums of neighborhoods
-        annotation_sums = annotations.sum(axis=0)  # Column sums of annotations
-    elif null_distribution == "annotations":
-        # Case 2: Only consider nodes with at least one annotation
-        annotated_nodes = (
-            np.ravel(annotations.sum(axis=1)) > 0
-        )  # Row-wise sum to filter nodes with annotations
-        background_population = annotated_nodes.sum()  # Total number of annotated nodes
-        neighborhood_sums = neighborhoods[annotated_nodes].sum(
-            axis=0
-        )  # Neighborhood sums for annotated nodes
-        annotation_sums = annotations[annotated_nodes].sum(
-            axis=0
-        )  # Annotation sums for annotated nodes
-    else:
-        raise ValueError(
-            "Invalid null_distribution value. Choose either 'network' or 'annotations'."
-        )
-
-    # Convert to dense arrays for downstream computations
-    neighborhood_sums = np.asarray(neighborhood_sums).reshape(-1, 1)  # Ensure column vector shape
-    annotation_sums = np.asarray(annotation_sums).reshape(1, -1)  # Ensure row vector shape
-
-    # Observed values: number of annotated nodes in each neighborhood
-    observed = neighborhoods.T @ annotations  # Shape: (neighborhoods, annotations)
-    # Expected values under the null
-    expected = (neighborhood_sums @ annotation_sums) / background_population
-    # Chi-squared statistic: sum((observed - expected)^2 / expected)
-    with np.errstate(divide="ignore", invalid="ignore"):  # Handle divide-by-zero
-        chi2_stat = np.where(expected > 0, np.power(observed - expected, 2) / expected, 0)
-
-    # Compute p-values for enrichment (upper tail) and depletion (lower tail)
-    enrichment_pvals = chi2.sf(chi2_stat, df=1)  # Survival function for upper tail
-    depletion_pvals = chi2.cdf(chi2_stat, df=1)  # Cumulative distribution for lower tail
-
-    return {"depletion_pvals": depletion_pvals, "enrichment_pvals": enrichment_pvals}
-
-
-def compute_hypergeom_test(
-    neighborhoods: csr_matrix,
-    annotations: csr_matrix,
-    null_distribution: str = "network",
-) -> Dict[str, Any]:
-    """
-    Compute hypergeometric test for enrichment and depletion in neighborhoods with selectable null distribution.
-
-    Args:
-        neighborhoods (csr_matrix): Sparse binary matrix representing neighborhoods.
-        annotations (csr_matrix): Sparse binary matrix representing annotations.
-        null_distribution (str, optional): Type of null distribution ('network' or 'annotations'). Defaults to "network".
-
-    Returns:
-        Dict[str, Any]: Dictionary containing depletion and enrichment p-values.
-    """
-    # Get the total number of nodes in the network
-    total_nodes = neighborhoods.shape[1]
-
-    # Compute sums
-    neighborhood_sums = neighborhoods.sum(axis=0).A.flatten()  # Convert to dense array
-    annotation_sums = annotations.sum(axis=0).A.flatten()  # Convert to dense array
-
-    if null_distribution == "network":
-        background_population = total_nodes
-    elif null_distribution == "annotations":
-        annotated_nodes = annotations.sum(axis=1).A.flatten() > 0  # Boolean mask
-        background_population = annotated_nodes.sum()
-        neighborhood_sums = neighborhoods[annotated_nodes].sum(axis=0).A.flatten()
-        annotation_sums = annotations[annotated_nodes].sum(axis=0).A.flatten()
-    else:
-        raise ValueError(
-            "Invalid null_distribution value. Choose either 'network' or 'annotations'."
-        )
-
-    # Observed counts
-    annotated_in_neighborhood = neighborhoods.T @ annotations  # Sparse result
-    annotated_in_neighborhood = annotated_in_neighborhood.toarray()  # Convert to dense
-    # Align shapes for broadcasting
-    neighborhood_sums = neighborhood_sums.reshape(-1, 1)
-    annotation_sums = annotation_sums.reshape(1, -1)
-    background_population = np.array(background_population).reshape(1, 1)
-
-    # Compute hypergeometric p-values
-    depletion_pvals = hypergeom.cdf(
-        annotated_in_neighborhood, background_population, annotation_sums, neighborhood_sums
-    )
-    enrichment_pvals = hypergeom.sf(
-        annotated_in_neighborhood - 1, background_population, annotation_sums, neighborhood_sums
-    )
-
-    return {"depletion_pvals": depletion_pvals, "enrichment_pvals": enrichment_pvals}
-
-
-def compute_poisson_test(
-    neighborhoods: csr_matrix,
-    annotations: csr_matrix,
-    null_distribution: str = "network",
-) -> Dict[str, Any]:
-    """
-    Compute Poisson test for enrichment and depletion in neighborhoods with selectable null distribution.
-
-    Args:
-        neighborhoods (csr_matrix): Sparse binary matrix representing neighborhoods.
-        annotations (csr_matrix): Sparse binary matrix representing annotations.
-        null_distribution (str, optional): Type of null distribution ('network' or 'annotations'). Defaults to "network".
-
-    Returns:
-        Dict[str, Any]: Dictionary containing depletion and enrichment p-values.
-    """
-    # Matrix multiplication to get the number of annotated nodes in each neighborhood
-    annotated_in_neighborhood = neighborhoods @ annotations  # Sparse result
-    # Convert annotated counts to dense for downstream calculations
-    annotated_in_neighborhood_dense = annotated_in_neighborhood.toarray()
-
-    # Compute lambda_expected based on the chosen null distribution
-    if null_distribution == "network":
-        # Use the mean across neighborhoods (axis=1)
-        lambda_expected = np.mean(annotated_in_neighborhood_dense, axis=1, keepdims=True)
-    elif null_distribution == "annotations":
-        # Use the mean across annotations (axis=0)
-        lambda_expected = np.mean(annotated_in_neighborhood_dense, axis=0, keepdims=True)
-    else:
-        raise ValueError(
-            "Invalid null_distribution value. Choose either 'network' or 'annotations'."
-        )
-
-    # Compute p-values for enrichment and depletion using Poisson distribution
-    enrichment_pvals = 1 - poisson.cdf(annotated_in_neighborhood_dense - 1, lambda_expected)
-    depletion_pvals = poisson.cdf(annotated_in_neighborhood_dense, lambda_expected)
-
-    return {"enrichment_pvals": enrichment_pvals, "depletion_pvals": depletion_pvals}
-
-
-def compute_zscore_test(
-    neighborhoods: csr_matrix,
-    annotations: csr_matrix,
-    null_distribution: str = "network",
-) -> Dict[str, Any]:
-    """
-    Compute z-score test for enrichment and depletion in neighborhoods with selectable null distribution.
-
-    Args:
-        neighborhoods (csr_matrix): Sparse binary matrix representing neighborhoods.
-        annotations (csr_matrix): Sparse binary matrix representing annotations.
-        null_distribution (str, optional): Type of null distribution ('network' or 'annotations'). Defaults to "network".
-
-    Returns:
-        Dict[str, Any]: Dictionary containing depletion and enrichment p-values.
-    """
-    # Total number of nodes in the network
-    total_node_count = neighborhoods.shape[1]
-
-    # Compute sums
-    if null_distribution == "network":
-        background_population = total_node_count
-        neighborhood_sums = neighborhoods.sum(axis=0).A.flatten()  # Dense column sums
-        annotation_sums = annotations.sum(axis=0).A.flatten()  # Dense row sums
-    elif null_distribution == "annotations":
-        annotated_nodes = annotations.sum(axis=1).A.flatten() > 0  # Dense boolean mask
-        background_population = annotated_nodes.sum()
-        neighborhood_sums = neighborhoods[annotated_nodes].sum(axis=0).A.flatten()
-        annotation_sums = annotations[annotated_nodes].sum(axis=0).A.flatten()
-    else:
-        raise ValueError(
-            "Invalid null_distribution value. Choose either 'network' or 'annotations'."
-        )
-
-    # Observed values
-    observed = (neighborhoods.T @ annotations).toarray()  # Convert sparse result to dense
-    # Expected values under the null
-    neighborhood_sums = neighborhood_sums.reshape(-1, 1)  # Ensure correct shape
-    annotation_sums = annotation_sums.reshape(1, -1)  # Ensure correct shape
-    expected = (neighborhood_sums @ annotation_sums) / background_population
-
-    # Standard deviation under the null
-    std_dev = np.sqrt(
-        expected
-        * (1 - annotation_sums / background_population)
-        * (1 - neighborhood_sums / background_population)
-    )
-    std_dev[std_dev == 0] = np.nan  # Avoid division by zero
-    # Compute z-scores
-    z_scores = (observed - expected) / std_dev
-
-    # Convert z-scores to depletion and enrichment p-values
-    enrichment_pvals = norm.sf(z_scores)  # Upper tail
-    depletion_pvals = norm.cdf(z_scores)  # Lower tail
-
-    return {"depletion_pvals": depletion_pvals, "enrichment_pvals": enrichment_pvals}

risk_network-0.0.11.dist-info/RECORD

@@ -1,41 +0,0 @@
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