mortis-spatial 0.1.0__py3-none-any.whl

mortis/__init__.py

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+"""
+MORTIS
+======
+Downstream analysis for spatial metabolomics (imaging mass spectrometry),
+on top of AnnData and scanpy.
+
+The short version of what it is for: an imaging run gives you tens of
+thousands of pixels per section, but a study has a handful of patients. Tests
+that treat pixels as replicates will report differences that are not there.
+Everything here that makes a claim about a group does it at the sample level.
+
+Typical workflow
+----------------
+>>> import mortis as mt
+>>>
+>>> # 1. Load and clean
+>>> adatas = mt.load_from_folder("./data")
+>>> clean, stats = mt.filter_background(adatas, cutoff=1.5, mode="sample")
+>>> adata = mt.merge_samples(clean, sample_col="section")
+>>> adata = mt.preprocess(adata)
+>>>
+>>> # 2. Look at it
+>>> adata = mt.cluster(adata)
+>>> mt.plot_spatial(adata, color="cluster")
+>>>
+>>> # 3. Test at the level of the patient, not the pixel
+>>> pb = mt.pseudobulk(adata, sample_key="section", carry_obs=["response"])
+>>> abundance = mt.differential_abundance(pb, "response", "R", "NR")
+>>>
+>>> # 4. Then ask whether the arrangement changed, not just the amount
+>>> org = mt.spatial_organization(adata, sample_key="section",
+...                               carry_obs=["response"])
+>>> layout = mt.differential_spatial_organization(org, "response", "R", "NR")
+>>>
+>>> # 5. Write down what was run, so the numbers can be checked later
+>>> mt.export_manifest(adata, "run/manifest.json")
+"""
+
+from __future__ import annotations
+
+from importlib.metadata import PackageNotFoundError as _PackageNotFoundError
+from importlib.metadata import version as _version
+
+try:
+    __version__ = _version("mortis-spatial")
+except _PackageNotFoundError:  # pragma: no cover - not installed, e.g. running from source
+    __version__ = "0.0.0+unknown"
+
+# Analysis
+from .analysis import (
+    batch_mixing_score,
+    cluster,
+    cluster_diversity,
+    cluster_nmf,
+    cluster_validation,
+    co_occurrence,
+    compare_clusterings,
+    compare_groups,
+    diversity_index,
+    find_markers,
+    getis_ord_gi,
+    lipid_class_summary,
+    local_moran,
+    merge_samples,
+    metabolite_colocalization,
+    metabolite_set_enrichment,
+    multi_group_test,
+    neighborhood_enrichment,
+    rename_clusters,
+    run_paga,
+    save_adata,
+    save_results,
+    score_metabolite_set,
+    spatial_autocorrelation,
+    spatial_de,
+    spatial_domains,
+    spatial_domains_kmeans,
+    spatial_gradient,
+    spatial_neighbors,
+    spatially_weighted_nmf,
+    split_by_obs,
+    subset_obs,
+    unmix_pixels,
+)
+
+# Annotation & enrichment
+from .annotate import (
+    CHEMICAL_CLASSES,
+    class_enrichment,
+    classification_report,
+    classify_compounds,
+    pathway_ora,
+)
+
+# Cross-cohort / longitudinal comparison
+from .compare import (
+    compare_signatures,
+    cross_cohort_profile,
+    track_flow,
+)
+
+# Exceptions
+from .exceptions import (
+    FileFormatError,
+    InsufficientSamplesError,
+    InvalidParameterError,
+    MissingROIError,
+    MissingSpatialError,
+    MortisError,
+    NoClustersError,
+    NoEmbeddingError,
+    NotPreprocessedError,
+    PseudoreplicationWarning,
+)
+
+# Filtering
+from .filter import (
+    filter_by_score,
+    filter_drugs,
+    list_drug_matches,
+)
+
+# Image (histology overlay)
+from .image import (
+    align_image,
+    extract_image_features,
+    load_image,
+    plot_image_overlay,
+)
+
+# Interactive
+from .interactive import (
+    draw_ROIs,
+    draw_ROIs_for_folder,
+)
+
+# I/O
+from .io import (
+    check_rois,
+    from_dataframe,
+    load_annotation_scores,
+    load_from_folder,
+    make_writable,
+    read_metabolomics_data,
+    save_spatial_data,
+)
+
+# Spatial organization (differential spatial pattern)
+from .organization import (
+    compare_abundance_and_organization,
+    differential_spatial_organization,
+    spatial_organization,
+)
+
+# Compound ID mapping & KEGG pathways (network)
+from .pathway import (
+    annotate_pathways,
+    clear_cache,
+    fetch_kegg_pathway_sets,
+    map_compound_ids,
+)
+
+# Plotting
+from .plotting import (
+    plot_cluster_composition,
+    plot_colocalization_network,
+    plot_embedding_grid,
+    plot_heatmap,
+    plot_markers,
+    plot_morans,
+    plot_qc,
+    plot_spatial,
+    plot_spatial_gradient,
+    plot_spatial_metabolite,
+    plot_umap,
+    plot_violin,
+    plot_volcano,
+)
+
+# Preprocessing
+from .preprocessing import (
+    correct_batches,
+    filter_background,
+    log1p_transform,
+    median_normalize,
+    preprocess,
+    run_harmony,
+    run_neighbors,
+    run_pca,
+    run_umap,
+    scale,
+    tic_normalize,
+)
+
+# Reproducibility manifests
+from .reproducibility import (
+    MANIFEST_VERSION,
+    data_fingerprint,
+    export_manifest,
+    provenance,
+    record_step,
+    result_fingerprint,
+    verify_manifest,
+)
+
+# Statistics (sample-level / patient-level)
+from .stats import (
+    cliffs_delta,
+    differential_abundance,
+    paired_differential_abundance,
+    pseudobulk,
+)
+
+# Publication figures & export
+from .viz import (
+    PALETTE,
+    diverging_cmap,
+    ion_cmap,
+    plot_abundance_vs_organization,
+    plot_class_enrichment,
+    plot_delta_volcano,
+    plot_effect_forest,
+    plot_effect_size,
+    plot_embedding,
+    plot_ion_images,
+    plot_organization_heatmap,
+    plot_pathway_dotplot,
+    plot_signature_comparison,
+    plot_spatial_panels,
+    reset_style,
+    save_figure,
+    set_publication_style,
+)
+
+__all__ = [
+    # Exceptions
+    "MortisError",
+    "MissingROIError",
+    "MissingSpatialError",
+    "NotPreprocessedError",
+    "NoClustersError",
+    "NoEmbeddingError",
+    "InsufficientSamplesError",
+    "InvalidParameterError",
+    "FileFormatError",
+    "PseudoreplicationWarning",
+
+    # I/O
+    "read_metabolomics_data",
+    "from_dataframe",
+    "make_writable",
+    "load_from_folder",
+    "load_annotation_scores",
+    "check_rois",
+    "save_spatial_data",
+
+    # Interactive
+    "draw_ROIs",
+    "draw_ROIs_for_folder",
+
+    # Preprocessing
+    "filter_background",
+    "tic_normalize",
+    "median_normalize",
+    "log1p_transform",
+    "scale",
+    "run_pca",
+    "run_neighbors",
+    "run_umap",
+    "correct_batches",
+    "run_harmony",
+    "preprocess",
+
+    # Filtering
+    "filter_by_score",
+    "filter_drugs",
+    "list_drug_matches",
+
+    # Image (histology overlay)
+    "load_image",
+    "align_image",
+    "extract_image_features",
+    "plot_image_overlay",
+
+    # Statistics (sample-level)
+    "pseudobulk",
+    "differential_abundance",
+    "paired_differential_abundance",
+    "cliffs_delta",
+
+    # Annotation & enrichment
+    "classify_compounds",
+    "classification_report",
+    "class_enrichment",
+    "pathway_ora",
+    "CHEMICAL_CLASSES",
+
+    # Reproducibility
+    "export_manifest",
+    "verify_manifest",
+    "record_step",
+    "provenance",
+    "data_fingerprint",
+    "result_fingerprint",
+    "MANIFEST_VERSION",
+
+    # Compound ID mapping & KEGG pathways
+    "map_compound_ids",
+    "fetch_kegg_pathway_sets",
+    "annotate_pathways",
+    "clear_cache",
+
+    # Publication figures & export
+    "set_publication_style",
+    "reset_style",
+    "save_figure",
+    "plot_effect_size",
+    "plot_effect_forest",
+    "plot_delta_volcano",
+    "plot_abundance_vs_organization",
+    "plot_signature_comparison",
+    "plot_ion_images",
+    "plot_spatial_panels",
+    "plot_embedding",
+    "plot_organization_heatmap",
+    "plot_class_enrichment",
+    "plot_pathway_dotplot",
+    "PALETTE",
+    "diverging_cmap",
+    "ion_cmap",
+
+    # Cross-cohort comparison
+    "cross_cohort_profile",
+    "track_flow",
+    "compare_signatures",
+
+    # Spatial organization
+    "spatial_organization",
+    "differential_spatial_organization",
+    "compare_abundance_and_organization",
+
+    # Analysis
+    "cluster",
+    "cluster_nmf",
+    "spatial_domains",
+    "spatial_domains_kmeans",
+    "rename_clusters",
+    "find_markers",
+    "compare_groups",
+    "multi_group_test",
+    "spatial_autocorrelation",
+    "spatial_de",
+    "local_moran",
+    "getis_ord_gi",
+    "spatial_neighbors",
+    "neighborhood_enrichment",
+    "co_occurrence",
+    "score_metabolite_set",
+    "metabolite_set_enrichment",
+    "lipid_class_summary",
+    "diversity_index",
+    "cluster_diversity",
+    "unmix_pixels",
+    "cluster_validation",
+    "compare_clusterings",
+    "batch_mixing_score",
+    "run_paga",
+    "subset_obs",
+    "merge_samples",
+    "split_by_obs",
+    "save_results",
+    "save_adata",
+
+    # Spatial structure
+    "spatially_weighted_nmf",
+    "spatial_gradient",
+    "metabolite_colocalization",
+
+    # Plotting
+    "plot_qc",
+    "plot_spatial",
+    "plot_spatial_metabolite",
+    "plot_embedding_grid",
+    "plot_umap",
+    "plot_markers",
+    "plot_volcano",
+    "plot_heatmap",
+    "plot_violin",
+    "plot_cluster_composition",
+    "plot_morans",
+
+    # Spatial structure plots
+    "plot_spatial_gradient",
+    "plot_colocalization_network",
+]