sphere-pca 0.3.0__py3-none-any.whl

pca_sphere_projection/__init__.py

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+"""Preserved manuscript-analysis namespace.
+
+The lightweight public API is :mod:`sphere_pca`. This historical namespace
+retains its original numerical implementation and requires the ``legacy``
+optional dependency set.
+"""
+
+from importlib import import_module
+
+
+_LEGACY_IMPORTS = {
+    "matplotlib.pyplot": "matplotlib",
+    "pandas": "pandas",
+    "plotly.graph_objects": "plotly",
+    "scipy.stats": "scipy",
+    "seaborn": "seaborn",
+    "statsmodels.stats.multitest": "statsmodels",
+}
+_missing_legacy_dependencies = []
+for _module, _distribution in _LEGACY_IMPORTS.items():
+    try:
+        import_module(_module)
+    except ModuleNotFoundError:
+        if _distribution not in _missing_legacy_dependencies:
+            _missing_legacy_dependencies.append(_distribution)
+
+if _missing_legacy_dependencies:
+    _missing = ", ".join(sorted(_missing_legacy_dependencies))
+    raise ImportError(
+        "The preserved pca_sphere_projection namespace requires optional "
+        f"legacy dependencies (missing: {_missing}). Install them with "
+        "`python -m pip install 'sphere-pca[legacy]'`. The lightweight "
+        "public API remains available as `import sphere_pca`."
+    )
+
+del _LEGACY_IMPORTS, _missing_legacy_dependencies, _module, _distribution
+
+from .comparison import (
+    conserved_stripe_test,
+    procrustes_align_spheres,
+    spherical_replicate_residual,
+)
+from .core import (
+    align_to_north_pole,
+    apply_euler_rotation,
+    equirectangular_projection,
+    find_and_visualize_correlated_genes,
+    statistical_test_on_lineages,
+    visualize_globe,
+    visualize_lineage_correlation,
+)
+from .perturbation import (
+    cluster_genes_by_perturbation_signature,
+    compute_gene_perturbation_vectors,
+    decompose_perturbation_vectors,
+    identify_sensitive_cells,
+    perturb_gene_expression,
+    plot_perturbation_vector_field,
+    project_expression_to_pca,
+    rank_genes_by_perturbation_magnitude,
+)
+from .robustness import (
+    compare_manual_vs_great_circle,
+    pc_coordinate_quality_summary,
+    root_sensitivity_analysis,
+    rotation_robustness_analysis,
+)
+from .sphere_stats import (
+    fit_great_circle,
+    geodesic_gradient,
+    horseshoe_null_test,
+    spherical_anisotropy,
+    spherical_kde,
+    stripe_strength_score,
+)
+from .stripe import (
+    detect_spherical_stripes,
+    multi_stripe_strength_score,
+    local_stripe_strength,
+    plot_detected_stripes,
+)
+from .pc_robustness import (
+    compute_scree_summary,
+    estimate_intrinsic_dimension,
+    compare_pc_count_spherical_geometry,
+    compare_top3_vs_random3_pcs,
+    compare_hvg_vs_all_gene_pc_geometry,
+)
+from .topology import (
+    build_spherical_knn_graph,
+    detect_branchpoints,
+    linear_vs_branching_score,
+)
+from .io import (
+    ExpressionData,
+    load_expression_matrix,
+    load_rds_expression,
+    load_bz2_klein_dataset,
+    load_celegan,
+    load_uc_epi,
+    load_hesc,
+    load_brca_atlas,
+    match_expression_to_pc_csv,
+)
+from .preprocessing import (
+    PCAResult,
+    normalize_log1p,
+    select_hvgs,
+    filter_genes,
+    fit_pca_embedding,
+    compare_hvg_vs_all_gene_pca,
+)
+from .entropy import (
+    compute_transcriptional_entropy,
+    compute_cytotrace_proxy,
+    compute_scent_proxy,
+    test_entropy_geodesic_gradient,
+)
+from .gene_geometry import (
+    compute_gene_geodesic_gradients,
+    compute_per_cell_gene_geodesic_gradient,
+    decompose_gene_gradient_theta_phi,
+    decompose_gene_gradient_relative_to_stripes,
+    rank_stripe_boundary_genes,
+    rank_stripe_boundary_genes_per_cell,
+    rank_along_trajectory_genes,
+    rank_along_trajectory_genes_per_cell,
+    filter_housekeeping_and_low_specificity_genes,
+    plot_gene_gradient_field,
+    plot_gene_gradient_on_sphere,
+    plot_gene_gradient_equirectangular,
+)
+from .known_regulators import (
+    REGULATOR_SETS,
+    get_regulator_set,
+    annotate_overlap,
+)
+
+__all__ = [
+    "align_to_north_pole",
+    "apply_euler_rotation",
+    "equirectangular_projection",
+    "visualize_globe",
+    "visualize_lineage_correlation",
+    "statistical_test_on_lineages",
+    "find_and_visualize_correlated_genes",
+    "stripe_strength_score",
+    "spherical_kde",
+    "geodesic_gradient",
+    "fit_great_circle",
+    "spherical_anisotropy",
+    "horseshoe_null_test",
+    "detect_spherical_stripes",
+    "multi_stripe_strength_score",
+    "local_stripe_strength",
+    "plot_detected_stripes",
+    "compute_scree_summary",
+    "estimate_intrinsic_dimension",
+    "compare_pc_count_spherical_geometry",
+    "compare_top3_vs_random3_pcs",
+    "compare_hvg_vs_all_gene_pc_geometry",
+    "build_spherical_knn_graph",
+    "detect_branchpoints",
+    "linear_vs_branching_score",
+    "procrustes_align_spheres",
+    "conserved_stripe_test",
+    "spherical_replicate_residual",
+    "project_expression_to_pca",
+    "perturb_gene_expression",
+    "compute_gene_perturbation_vectors",
+    "rank_genes_by_perturbation_magnitude",
+    "decompose_perturbation_vectors",
+    "identify_sensitive_cells",
+    "plot_perturbation_vector_field",
+    "cluster_genes_by_perturbation_signature",
+    "root_sensitivity_analysis",
+    "rotation_robustness_analysis",
+    "pc_coordinate_quality_summary",
+    "compare_manual_vs_great_circle",
+    # raw-expression validation
+    "ExpressionData",
+    "load_expression_matrix",
+    "load_rds_expression",
+    "load_bz2_klein_dataset",
+    "load_celegan",
+    "load_uc_epi",
+    "load_hesc",
+    "load_brca_atlas",
+    "match_expression_to_pc_csv",
+    "PCAResult",
+    "normalize_log1p",
+    "select_hvgs",
+    "filter_genes",
+    "fit_pca_embedding",
+    "compare_hvg_vs_all_gene_pca",
+    "compute_transcriptional_entropy",
+    "compute_cytotrace_proxy",
+    "compute_scent_proxy",
+    "test_entropy_geodesic_gradient",
+    "compute_gene_geodesic_gradients",
+    "compute_per_cell_gene_geodesic_gradient",
+    "decompose_gene_gradient_theta_phi",
+    "decompose_gene_gradient_relative_to_stripes",
+    "rank_stripe_boundary_genes",
+    "rank_stripe_boundary_genes_per_cell",
+    "rank_along_trajectory_genes",
+    "rank_along_trajectory_genes_per_cell",
+    "filter_housekeeping_and_low_specificity_genes",
+    "plot_gene_gradient_field",
+    "plot_gene_gradient_on_sphere",
+    "plot_gene_gradient_equirectangular",
+    "REGULATOR_SETS",
+    "get_regulator_set",
+    "annotate_overlap",
+]