from .io import (
    load_mode_alignment,
    load_mode_stats,
    load_aligned_Qs,
    load_input_meta,
    load_unaligned_for_modes,
    load_alignment_across_K,
    load_all_modes_alignment,
    group_modes_by_K,
    infer_K_range,
    load_clumppling_results,
    load_compmodels_results,
    add_pairwise_alignment,
    subset_compmodels,
    load_gene_set,
    load_gene_intervals,
    filter_bed_by_peaks,
    filter_gene_links_by_ccre,
)
from .wrappers import (
    run_clumppling,
    prepare_compmodels,
    run_comp_models,
)
from .analysis import (
    subset_results,
    compute_profile,
    get_sepLFC,
    compute_weighted_Psum,
    compute_feature_metrics,
    compute_all_feature_metrics,
    select_top_features,
    analyze_sep_genes,
    get_mode_pair_mappings,
    map_alt_to_ref,
)
from .membership import (
    compute_membership_diff,
    compute_per_cell_diff,
    get_diff_matrices,
    get_pairwise_diff,
    get_pairwise_membership_diff,
    get_group_indices,
    compute_group_sizes,
    compute_group_diff,
    compute_mode_diffs,
    compute_all_mode_diffs,
    build_diff_df,
    compute_avg_memberships,
    compute_fstruct,
    compute_fstruct_by_group,
    compute_fstruct_by_model_group,
    bootstrap_fstruct_by_group,
    bootstrap_fstruct_by_model_group,
    get_mode_sizes,
)
from .genomics import (
    match_peaks_to_genes,
    peaks_with_top_gene_overlap,
    make_col_unique,
)
from .enrichment import (
    resolve_gene_set,
    sample_null_P,
    test_P_enrichment,
    test_LFC_enrichment,
    test_sepLFC_enrichment,
    compute_gene_lfc,
    run_gs_enrichment,
)
from .plot import (
    plot_Q_heatmap,
    plot_Q_grid,
    plot_cluster_bars,
    plot_cluster_scatter,
    plot_spatial_membership,
    plot_feature_scatter,
    plot_feature_kde,
    get_kde_outliers,
    plot_feature_bar,
    plot_P_profile,
    plot_mode_P_profile,
    plot_sepLFC_dist,
    plot_cluster_in_grid,
    plot_cluster_panels,
    plot_cluster_overlay,
    plot_sepLFC_labels,
    plot_feature_metrics,
    plot_feature_across_modes,
    plot_feature_sepLFC_across_modes,
    make_mode_grid,
    make_mode_grid_by_K,
)
from .plot_comparison import (
    plot_compmodels_Q_grid,
    plot_compmodels_Q_selected,
    plot_compmodels_diff_grid,
    plot_compmodels_diff_selected,
    plot_model_diff_summary,
    plot_compmodels_alignment_list,
    plot_compmodels_alignment_by_model,
    plot_discrete_colorbar,
    plot_group_diff,
    plot_mapping_grid,
    plot_mapping_alignment,
    plot_model_diff_heatmap,
    plot_avg_membership_barh,
    plot_feature_count,
    plot_membership_reordered,
    plot_structure_two_level,
    plot_structure_one_level,
    plot_spatial_structure_grid,
    plot_feature_cluster_panels,
)
from .plot_enrichment import (
    plot_pairwise_heatmap,
    plot_pairwise_heatmap_bidir,
    plot_P_enrichment_heatmap,
    plot_LFC_enrichment_heatmap,
    plot_top_pairwise_df,
    plot_P_enrichment_pval,
    plot_P_enrichment_zscore,
    plot_sepLFC_null_sep,
    plot_sepLFC_null_fixed,
    plot_sepLFC_distribution,
    plot_gene_P_bars,
    plot_gene_P_stacked,
    plot_per_cluster_P,
    plot_seplfc_bipartite,
    plot_gene_lfc,
    plot_P_enrichment_grid,
    plot_LFC_enrichment_grid,
    plot_sepLFC_enrichment_grid,
    plot_P_enrichment_by_cluster,
    plot_sepLFC_distribution_heatmap,
)

__all__ = [
    "run_clumppling",
    "prepare_compmodels",
    "run_comp_models",
    "load_mode_alignment",
    "load_mode_stats",
    "load_aligned_Qs",
    "load_input_meta",
    "load_unaligned_for_modes",
    "load_alignment_across_K",
    "load_all_modes_alignment",
    "group_modes_by_K",
    "infer_K_range",
    "load_clumppling_results",
    "load_compmodels_results",
    "add_pairwise_alignment",
    "subset_compmodels",
    "load_gene_set",
    "load_gene_intervals",
    "filter_bed_by_peaks",
    "filter_gene_links_by_ccre",
    "subset_results",
    "compute_profile",
    "get_sepLFC",
    "compute_weighted_Psum",
    "compute_feature_metrics",
    "compute_all_feature_metrics",
    "select_top_features",
    "analyze_sep_genes",
    "get_mode_pair_mappings",
    "map_alt_to_ref",
    "compute_membership_diff",
    "compute_per_cell_diff",
    "get_diff_matrices",
    "get_pairwise_diff",
    "get_pairwise_membership_diff",
    "get_group_indices",
    "compute_group_sizes",
    "compute_group_diff",
    "compute_mode_diffs",
    "compute_all_mode_diffs",
    "build_diff_df",
    "compute_avg_memberships",
    "compute_fstruct",
    "compute_fstruct_by_group",
    "compute_fstruct_by_model_group",
    "bootstrap_fstruct_by_group",
    "bootstrap_fstruct_by_model_group",
    "get_mode_sizes",
    "match_peaks_to_genes",
    "peaks_with_top_gene_overlap",
    "make_col_unique",
    "resolve_gene_set",
    "sample_null_P",
    "test_P_enrichment",
    "test_LFC_enrichment",
    "test_sepLFC_enrichment",
    "compute_gene_lfc",
    "run_gs_enrichment",
    "plot_Q_heatmap",
    "plot_Q_grid",
    "plot_cluster_bars",
    "plot_cluster_scatter",
    "plot_spatial_membership",
    "plot_feature_scatter",
    "plot_feature_kde",
    "get_kde_outliers",
    "plot_feature_bar",
    "plot_P_profile",
    "plot_mode_P_profile",
    "plot_sepLFC_dist",
    "make_mode_grid",
    "make_mode_grid_by_K",
    "plot_cluster_in_grid",
    "plot_cluster_panels",
    "plot_cluster_overlay",
    "plot_sepLFC_labels",
    "plot_feature_metrics",
    "plot_feature_across_modes",
    "plot_feature_sepLFC_across_modes",
    "plot_compmodels_Q_grid",
    "plot_compmodels_Q_selected",
    "plot_compmodels_diff_grid",
    "plot_compmodels_diff_selected",
    "plot_model_diff_summary",
    "plot_compmodels_alignment_list",
    "plot_compmodels_alignment_by_model",
    "plot_discrete_colorbar",
    "plot_group_diff",
    "plot_mapping_grid",
    "plot_mapping_alignment",
    "plot_model_diff_heatmap",
    "plot_avg_membership_barh",
    "plot_feature_count",
    "plot_membership_reordered",
    "plot_structure_two_level",
    "plot_structure_one_level",
    "plot_spatial_structure_grid",
    "plot_feature_cluster_panels",
    "plot_pairwise_heatmap",
    "plot_pairwise_heatmap_bidir",
    "plot_P_enrichment_heatmap",
    "plot_LFC_enrichment_heatmap",
    "plot_top_pairwise_df",
    "plot_P_enrichment_pval",
    "plot_P_enrichment_zscore",
    "plot_sepLFC_null_sep",
    "plot_sepLFC_null_fixed",
    "plot_sepLFC_distribution",
    "plot_gene_P_bars",
    "plot_gene_P_stacked",
    "plot_per_cluster_P",
    "plot_seplfc_bipartite",
    "plot_gene_lfc",
    "plot_P_enrichment_grid",
    "plot_LFC_enrichment_grid",
    "plot_sepLFC_enrichment_grid",
    "plot_P_enrichment_by_cluster",
    "plot_sepLFC_distribution_heatmap",
]
