@bgicli/bgicli 2.1.1 → 2.2.0

package/data/workflows/spatial-transcriptomics/scripts/export_results.py

@@ -0,0 +1,214 @@
+"""
+============================================================================
+EXPORT SPATIAL ANALYSIS RESULTS
+============================================================================
+
+Functions:
+  - export_all(): Export all results from spatial analysis
+
+Usage:
+  from export_results import export_all
+  export_all(adata, output_dir="visium_results")
+"""
+
+import os
+import numpy as np
+import pandas as pd
+from pathlib import Path
+from datetime import datetime
+
+
+def export_all(
+    adata: 'anndata.AnnData',
+    output_dir: str = "visium_results"
+) -> None:
+    """
+    Export all spatial transcriptomics analysis results.
+
+    Exports:
+    1. adata_processed.h5ad — complete processed AnnData (CRITICAL)
+    2. spatially_variable_genes.csv — SVGs with Moran's I statistics
+    3. cluster_assignments.csv — spot barcodes + cluster + spatial coords
+    4. neighborhood_enrichment.csv — cluster-cluster enrichment z-scores
+    5. spot_metadata.csv — all obs columns
+    6. analysis_summary.txt — human-readable report
+
+    Parameters
+    ----------
+    adata : AnnData
+        Processed AnnData from run_spatial_analysis().
+    output_dir : str
+        Output directory (default: "visium_results").
+    """
+    print("\n=== Step 4: Export Results ===\n")
+
+    output_dir = Path(output_dir)
+    output_dir.mkdir(parents=True, exist_ok=True)
+
+    # --- 1. Save processed h5ad (CRITICAL for downstream skills) ---
+    print("1. Saving processed AnnData object...")
+    h5ad_path = output_dir / "adata_processed.h5ad"
+    adata_save = adata.copy()
+    # Clean uns for h5ad serialization (remove non-serializable objects)
+    _clean_uns_for_h5ad(adata_save)
+    adata_save.write_h5ad(h5ad_path, compression='gzip')
+    file_size_mb = h5ad_path.stat().st_size / (1024 * 1024)
+    print(f"   ✓ {h5ad_path} ({file_size_mb:.1f} MB)")
+    print(f"   (Load with: adata = sc.read_h5ad('adata_processed.h5ad'))")
+
+    # --- 2. Spatially variable genes ---
+    print("\n2. Exporting spatially variable genes...")
+    svg_results = adata.uns.get('svg_results', None)
+    if svg_results is not None and len(svg_results) > 0:
+        svg_path = output_dir / "spatially_variable_genes.csv"
+        svg_results.to_csv(svg_path)
+        print(f"   ✓ {svg_path} ({len(svg_results)} genes)")
+    else:
+        print("   (No SVG results to export)")
+
+    # --- 3. Cluster assignments with spatial coordinates ---
+    print("\n3. Exporting cluster assignments...")
+    cluster_df = pd.DataFrame({
+        'barcode': adata.obs_names,
+        'cluster': adata.obs['leiden'].values,
+        'spatial_x': adata.obsm['spatial'][:, 0],
+        'spatial_y': adata.obsm['spatial'][:, 1],
+    })
+    if 'total_counts' in adata.obs.columns:
+        cluster_df['total_counts'] = adata.obs['total_counts'].values
+    if 'n_genes_by_counts' in adata.obs.columns:
+        cluster_df['n_genes'] = adata.obs['n_genes_by_counts'].values
+    cluster_path = output_dir / "cluster_assignments.csv"
+    cluster_df.to_csv(cluster_path, index=False)
+    print(f"   ✓ {cluster_path} ({len(cluster_df)} spots)")
+
+    # --- 4. Neighborhood enrichment ---
+    print("\n4. Exporting neighborhood enrichment...")
+    if 'leiden_nhood_enrichment' in adata.uns:
+        zscore = adata.uns['leiden_nhood_enrichment']['zscore']
+        clusters = sorted(adata.obs['leiden'].unique(), key=int)
+        labels = [str(c) for c in clusters]
+        nhood_df = pd.DataFrame(zscore, index=labels, columns=labels)
+        nhood_path = output_dir / "neighborhood_enrichment.csv"
+        nhood_df.to_csv(nhood_path)
+        print(f"   ✓ {nhood_path}")
+    else:
+        print("   (No neighborhood enrichment results)")
+
+    # --- 5. Full spot metadata ---
+    print("\n5. Exporting spot metadata...")
+    metadata_path = output_dir / "spot_metadata.csv"
+    adata.obs.to_csv(metadata_path)
+    print(f"   ✓ {metadata_path} ({len(adata.obs)} spots, {len(adata.obs.columns)} columns)")
+
+    # --- 6. Analysis summary ---
+    print("\n6. Generating analysis summary...")
+    _write_summary(adata, output_dir)
+    print(f"   ✓ {output_dir / 'analysis_summary.txt'}")
+
+    # Final verification
+    print("\n" + "=" * 50)
+    print("=== Export Complete ===")
+    print("=" * 50)
+    print(f"\nAll results saved to: {output_dir}/")
+    print(f"\nKey outputs:")
+    print(f"  - adata_processed.h5ad   (Load with: adata = sc.read_h5ad(...))")
+    print(f"  - spatially_variable_genes.csv")
+    print(f"  - cluster_assignments.csv")
+    print(f"  - neighborhood_enrichment.csv")
+    print(f"  - spot_metadata.csv")
+    print(f"  - analysis_summary.txt")
+
+
+def _clean_uns_for_h5ad(adata) -> None:
+    """Remove non-serializable objects from uns for h5ad export."""
+    keys_to_check = list(adata.uns.keys())
+    for key in keys_to_check:
+        val = adata.uns[key]
+        # Convert numpy int/float to Python native
+        if isinstance(val, dict):
+            adata.uns[key] = _convert_dict_types(val)
+        elif isinstance(val, pd.DataFrame):
+            pass  # DataFrames are fine
+        elif isinstance(val, np.ndarray):
+            pass  # Arrays are fine
+        elif isinstance(val, (np.integer, np.floating)):
+            adata.uns[key] = val.item()
+
+
+def _convert_dict_types(d: dict) -> dict:
+    """Convert numpy types in dict to native Python for JSON serialization."""
+    result = {}
+    for k, v in d.items():
+        if isinstance(v, (np.integer,)):
+            result[k] = int(v)
+        elif isinstance(v, (np.floating,)):
+            result[k] = float(v)
+        elif isinstance(v, np.ndarray):
+            result[k] = v
+        elif isinstance(v, dict):
+            result[k] = _convert_dict_types(v)
+        else:
+            result[k] = v
+    return result
+
+
+def _write_summary(adata, output_dir: Path) -> None:
+    """Write human-readable analysis summary."""
+    params = adata.uns.get('spatial_analysis_params', {})
+
+    with open(output_dir / 'analysis_summary.txt', 'w') as f:
+        f.write("=" * 70 + "\n")
+        f.write("SPATIAL TRANSCRIPTOMICS ANALYSIS SUMMARY\n")
+        f.write(f"Generated: {datetime.now().strftime('%Y-%m-%d %H:%M:%S')}\n")
+        f.write("=" * 70 + "\n\n")
+
+        f.write("DATASET\n")
+        f.write("-" * 70 + "\n")
+        f.write(f"Spots (after QC):  {adata.n_obs}\n")
+        f.write(f"Genes:             {adata.n_vars}\n")
+        f.write(f"Clusters (Leiden): {params.get('n_clusters', 'N/A')}\n")
+        f.write(f"SVGs (FDR < 0.05): {params.get('n_svgs', 'N/A')}\n\n")
+
+        f.write("QC FILTERING\n")
+        f.write("-" * 70 + "\n")
+        f.write(f"Initial spots:     {params.get('n_spots_initial', 'N/A')}\n")
+        f.write(f"After filtering:   {params.get('n_spots_after', 'N/A')}\n")
+        n_init = params.get('n_spots_initial', 0)
+        n_after = params.get('n_spots_after', 0)
+        if n_init > 0:
+            f.write(f"Retention:         {100 * n_after / n_init:.1f}%\n")
+        f.write(f"min_genes:         {params.get('min_genes', 'N/A')}\n")
+        f.write(f"max_pct_mito:      {params.get('max_pct_mito', 'N/A')}%\n\n")
+
+        f.write("ANALYSIS PARAMETERS\n")
+        f.write("-" * 70 + "\n")
+        f.write(f"HVGs:              {params.get('n_top_genes', 'N/A')}\n")
+        f.write(f"PCA components:    {params.get('n_pcs', 'N/A')}\n")
+        f.write(f"Leiden resolution: {params.get('resolution', 'N/A')}\n")
+        f.write(f"SVG permutations:  {params.get('svgs_n_perms', 'N/A')}\n\n")
+
+        # Cluster distribution
+        if 'leiden' in adata.obs.columns:
+            f.write("CLUSTER DISTRIBUTION\n")
+            f.write("-" * 70 + "\n")
+            for cluster in sorted(adata.obs['leiden'].unique(), key=int):
+                count = (adata.obs['leiden'] == cluster).sum()
+                pct = 100 * count / adata.n_obs
+                f.write(f"  Cluster {cluster:>3}: {count:>5} spots ({pct:>5.1f}%)\n")
+            f.write("\n")
+
+        # Top SVGs
+        svg_results = adata.uns.get('svg_results', None)
+        if svg_results is not None and len(svg_results) > 0:
+            f.write("TOP SPATIALLY VARIABLE GENES\n")
+            f.write("-" * 70 + "\n")
+            top20 = svg_results.head(20)
+            for gene, row in top20.iterrows():
+                f.write(f"  {gene:<15} Moran's I = {row['I']:.4f}  "
+                        f"FDR = {row['pval_norm_fdr_bh']:.2e}\n")
+            f.write("\n")
+
+        f.write("=" * 70 + "\n")
+        f.write("Pipeline: Squidpy + Scanpy spatial transcriptomics analysis\n")
+        f.write("=" * 70 + "\n")

package/data/workflows/spatial-transcriptomics/scripts/generate_all_plots.py

@@ -0,0 +1,397 @@
+"""
+============================================================================
+SPATIAL TRANSCRIPTOMICS VISUALIZATION
+============================================================================
+
+Generate publication-quality plots for spatial analysis results.
+Uses plotnine + theme_prism() for standard plots, seaborn for heatmaps,
+and scanpy/squidpy for spatial tissue overlays.
+
+Functions:
+  - generate_all_plots(): Generate all visualizations (PNG + SVG)
+
+Usage:
+  from generate_all_plots import generate_all_plots
+  generate_all_plots(adata, output_dir="visium_results")
+"""
+
+import numpy as np
+import pandas as pd
+import matplotlib
+matplotlib.use('Agg')
+import matplotlib.pyplot as plt
+import seaborn as sns
+from pathlib import Path
+from typing import Optional, List, Union
+
+from plotnine import (
+    ggplot, aes, geom_violin, geom_jitter, geom_point, geom_col,
+    geom_line, labs, theme, coord_flip, facet_wrap, element_text,
+    element_blank, scale_color_cmap, guides, guide_legend,
+    scale_fill_hue, scale_color_hue
+)
+from plotnine_prism import theme_prism
+
+
+# ---------------------------------------------------------------------------
+# Save helper: PNG + SVG with graceful fallback
+# ---------------------------------------------------------------------------
+
+def _save_plot(fig, base_path: Union[str, Path], dpi: int = 300,
+               width: float = 8, height: float = 6) -> None:
+    """Save plot in PNG + SVG with graceful SVG fallback."""
+    base_path = Path(base_path)
+    base_no_ext = base_path.with_suffix('')
+
+    # Always save PNG
+    png_path = base_no_ext.with_suffix('.png')
+    try:
+        if hasattr(fig, 'save'):  # plotnine
+            fig.save(str(png_path), width=width, height=height, dpi=dpi, verbose=False)
+        else:  # matplotlib figure
+            fig.savefig(str(png_path), dpi=dpi, bbox_inches='tight', format='png')
+        print(f"   Saved: {png_path}")
+    except Exception as e:
+        print(f"   Warning: PNG export failed: {e}")
+
+    # Always try SVG
+    svg_path = base_no_ext.with_suffix('.svg')
+    try:
+        if hasattr(fig, 'save'):  # plotnine
+            fig.save(str(svg_path), width=width, height=height, verbose=False)
+        else:  # matplotlib figure
+            fig.savefig(str(svg_path), bbox_inches='tight', format='svg')
+        print(f"   Saved: {svg_path}")
+    except Exception:
+        print(f"   (SVG export failed)")
+
+
+def _save_matplotlib(fig, base_path, dpi=300, width=8, height=6):
+    """Save matplotlib figure and close it."""
+    _save_plot(fig, base_path, dpi=dpi, width=width, height=height)
+    plt.close(fig)
+
+
+# ---------------------------------------------------------------------------
+# Individual plot functions
+# ---------------------------------------------------------------------------
+
+def _plot_qc_violins(adata, output_dir: Path) -> None:
+    """QC violin plots using plotnine + theme_prism."""
+    qc_df = pd.DataFrame({
+        'Total Counts': adata.obs['total_counts'].values,
+        'Genes Detected': adata.obs['n_genes_by_counts'].values,
+        'Mitochondrial %': adata.obs['pct_counts_mt'].values,
+    })
+    qc_long = qc_df.melt(var_name='Metric', value_name='Value')
+
+    p = (
+        ggplot(qc_long, aes(x='Metric', y='Value'))
+        + geom_violin(fill='#4C72B0', alpha=0.7)
+        + facet_wrap('~Metric', scales='free')
+        + labs(title='QC Metrics', x='', y='Value')
+        + theme_prism(base_size=12)
+        + theme(
+            plot_title=element_text(hjust=0.5, face='bold', size=14),
+            axis_text_x=element_blank(),
+            strip_text=element_text(size=11, face='bold'),
+        )
+    )
+    _save_plot(p, output_dir / 'qc_violins.png', width=12, height=5)
+    print("  ✓ QC violin plots saved")
+
+
+def _plot_spatial_clusters(adata, output_dir: Path) -> None:
+    """Spatial cluster overlay using scanpy."""
+    import scanpy as sc
+
+    fig, ax = plt.subplots(1, 1, figsize=(8, 8))
+    sc.pl.spatial(
+        adata, color='leiden', ax=ax, show=False,
+        title='Spatial Clusters (Leiden)',
+        frameon=False, spot_size=1.5
+    )
+    _save_matplotlib(fig, output_dir / 'spatial_clusters.png', width=8, height=8)
+    print("  ✓ Spatial cluster plot saved")
+
+
+def _plot_spatial_markers(adata, marker_genes: List[str], output_dir: Path) -> None:
+    """Spatial marker gene expression using scanpy."""
+    import scanpy as sc
+
+    n_genes = len(marker_genes)
+    ncols = min(3, n_genes)
+    nrows = (n_genes + ncols - 1) // ncols
+
+    fig, axes = plt.subplots(nrows, ncols, figsize=(6 * ncols, 5.5 * nrows))
+    if n_genes == 1:
+        axes = np.array([axes])
+    axes = axes.flatten()
+
+    for i, gene in enumerate(marker_genes):
+        sc.pl.spatial(
+            adata, color=gene, ax=axes[i], show=False,
+            title=gene, frameon=False, spot_size=1.5,
+            cmap='Reds'
+        )
+
+    # Hide unused axes
+    for j in range(n_genes, len(axes)):
+        axes[j].set_visible(False)
+
+    fig.suptitle('Marker Gene Expression', fontsize=14, fontweight='bold', y=1.02)
+    fig.tight_layout()
+    _save_matplotlib(fig, output_dir / 'spatial_markers.png',
+                     width=6 * ncols, height=5.5 * nrows)
+    print(f"  ✓ Spatial marker plots saved ({n_genes} genes)")
+
+
+def _plot_umap_clusters(adata, output_dir: Path) -> None:
+    """UMAP by cluster using plotnine + theme_prism."""
+    umap_df = pd.DataFrame(
+        adata.obsm['X_umap'],
+        columns=['UMAP1', 'UMAP2']
+    )
+    umap_df['Cluster'] = adata.obs['leiden'].values
+
+    p = (
+        ggplot(umap_df, aes(x='UMAP1', y='UMAP2', color='Cluster'))
+        + geom_point(size=0.5, alpha=0.7)
+        + labs(title='UMAP (Leiden Clusters)', color='Cluster')
+        + theme_prism(base_size=12)
+        + theme(
+            plot_title=element_text(hjust=0.5, face='bold', size=14),
+        )
+        + guides(color=guide_legend(override_aes={'size': 3}))
+    )
+    _save_plot(p, output_dir / 'umap_clusters.png', width=9, height=7)
+    print("  ✓ UMAP cluster plot saved")
+
+
+def _plot_nhood_enrichment(adata, output_dir: Path) -> None:
+    """Neighborhood enrichment heatmap using seaborn.clustermap."""
+    zscore = adata.uns['leiden_nhood_enrichment']['zscore']
+    clusters = sorted(adata.obs['leiden'].unique(), key=int)
+    labels = [str(c) for c in clusters]
+
+    zscore_df = pd.DataFrame(zscore, index=labels, columns=labels)
+
+    g = sns.clustermap(
+        zscore_df,
+        cmap='RdBu_r',
+        center=0,
+        figsize=(10, 9),
+        cbar_kws={'label': 'Enrichment Z-score'},
+        dendrogram_ratio=0.1,
+        linewidths=0.5,
+        linecolor='white',
+    )
+    g.ax_heatmap.set_xlabel('Cluster', fontsize=12)
+    g.ax_heatmap.set_ylabel('Cluster', fontsize=12)
+    g.fig.suptitle('Neighborhood Enrichment', fontsize=14, fontweight='bold', y=1.02)
+
+    _save_matplotlib(g.fig, output_dir / 'neighborhood_enrichment.png', width=10, height=9)
+    print("  ✓ Neighborhood enrichment heatmap saved")
+
+
+def _plot_co_occurrence(adata, output_dir: Path) -> None:
+    """Co-occurrence probability vs distance using plotnine + theme_prism."""
+    co_occ = adata.uns['leiden_co_occurrence']
+    occ = co_occ['occ']
+    interval = co_occ['interval']
+
+    # Midpoints of distance intervals
+    midpoints = [(interval[i] + interval[i + 1]) / 2 for i in range(len(interval) - 1)]
+
+    clusters = sorted(adata.obs['leiden'].unique(), key=int)
+    n_clusters = len(clusters)
+
+    # Build long-form DataFrame for plotnine
+    rows = []
+    for i in range(min(n_clusters, 8)):
+        for j, d in enumerate(midpoints):
+            rows.append({
+                'Distance': d,
+                'Co-occurrence': occ[i, i, j],
+                'Cluster': str(clusters[i])
+            })
+    co_df = pd.DataFrame(rows)
+
+    p = (
+        ggplot(co_df, aes(x='Distance', y='Co-occurrence', color='Cluster'))
+        + geom_line(size=1.2, alpha=0.8)
+        + labs(
+            title='Cluster Co-occurrence by Distance',
+            x='Distance', y='Co-occurrence Probability',
+            color='Cluster'
+        )
+        + theme_prism(base_size=12)
+        + theme(
+            plot_title=element_text(hjust=0.5, face='bold', size=14),
+        )
+    )
+    _save_plot(p, output_dir / 'co_occurrence.png', width=10, height=6)
+    print("  ✓ Co-occurrence plot saved")
+
+
+def _plot_top_svgs(svg_results: pd.DataFrame, top_n: int, output_dir: Path) -> None:
+    """Top spatially variable genes bar chart using plotnine + theme_prism."""
+    top_svgs = svg_results.head(top_n).copy()
+    top_svgs['Gene'] = top_svgs.index
+    # Reverse for horizontal bar chart (highest at top)
+    top_svgs['Gene'] = pd.Categorical(
+        top_svgs['Gene'], categories=top_svgs['Gene'][::-1], ordered=True
+    )
+
+    p = (
+        ggplot(top_svgs, aes(x='Gene', y='I'))
+        + geom_col(fill='#4C72B0', alpha=0.85)
+        + coord_flip()
+        + labs(
+            title=f"Top {top_n} Spatially Variable Genes",
+            x='', y="Moran's I"
+        )
+        + theme_prism(base_size=12)
+        + theme(
+            plot_title=element_text(hjust=0.5, face='bold', size=14),
+        )
+    )
+    _save_plot(p, output_dir / 'top_svgs.png', width=8, height=6)
+    print("  ✓ Top SVGs bar plot saved")
+
+
+def _plot_spatial_svg(adata, gene: str, output_dir: Path) -> None:
+    """Spatial expression of top SVG using scanpy."""
+    import scanpy as sc
+
+    fig, ax = plt.subplots(1, 1, figsize=(8, 8))
+    sc.pl.spatial(
+        adata, color=gene, ax=ax, show=False,
+        title=f'{gene} (Top SVG)', frameon=False,
+        spot_size=1.5, cmap='magma'
+    )
+    _save_matplotlib(fig, output_dir / f'spatial_svg_{gene}.png', width=8, height=8)
+    print(f"  ✓ Spatial SVG plot saved ({gene})")
+
+
+# ---------------------------------------------------------------------------
+# Main entry point
+# ---------------------------------------------------------------------------
+
+def generate_all_plots(
+    adata: 'anndata.AnnData',
+    output_dir: str = "visium_results",
+    marker_genes: Optional[List[str]] = None,
+    top_n_svgs: int = 10
+) -> None:
+    """
+    Generate all spatial transcriptomics visualizations.
+
+    Plots (all PNG + SVG):
+    1. QC violin plots (total_counts, n_genes, pct_mito) — plotnine
+    2. Spatial scatter — clusters on tissue — scanpy
+    3. Spatial scatter — marker genes — scanpy
+    4. UMAP colored by cluster — plotnine
+    5. Neighborhood enrichment heatmap — seaborn.clustermap
+    6. Co-occurrence plot — matplotlib
+    7. Top SVGs bar chart — plotnine
+    8. Spatial scatter of top SVG — scanpy
+
+    Parameters
+    ----------
+    adata : AnnData
+        Processed AnnData from run_spatial_analysis().
+    output_dir : str
+        Output directory (default: "visium_results").
+    marker_genes : list of str, optional
+        Genes for tissue overlay (default: cardiac markers).
+    top_n_svgs : int
+        Number of top SVGs for bar plot (default: 10).
+    """
+    output_dir = Path(output_dir)
+    output_dir.mkdir(parents=True, exist_ok=True)
+
+    print("\n=== Step 3: Generate Visualizations ===\n")
+
+    # Default cardiac marker genes
+    if marker_genes is None:
+        marker_genes = ['MYH7', 'TNNI3', 'MYH6', 'NPPA', 'TTN', 'ACTN2']
+
+    # Filter to available markers
+    available_markers = [g for g in marker_genes if g in adata.var_names]
+
+    # --- 1. QC violin plots ---
+    print("1. Generating QC violin plots...")
+    try:
+        _plot_qc_violins(adata, output_dir)
+    except Exception as e:
+        print(f"   Error: {e}")
+
+    # --- 2. Spatial clusters ---
+    print("2. Generating spatial cluster plot...")
+    try:
+        _plot_spatial_clusters(adata, output_dir)
+    except Exception as e:
+        print(f"   Error: {e}")
+
+    # --- 3. Spatial markers ---
+    if available_markers:
+        print(f"3. Generating spatial marker gene plots ({len(available_markers)} genes)...")
+        try:
+            _plot_spatial_markers(adata, available_markers, output_dir)
+        except Exception as e:
+            print(f"   Error: {e}")
+    else:
+        print("3. Skipping marker gene plots (no matching genes in dataset)")
+
+    # --- 4. UMAP ---
+    print("4. Generating UMAP cluster plot...")
+    try:
+        _plot_umap_clusters(adata, output_dir)
+    except Exception as e:
+        print(f"   Error: {e}")
+
+    # --- 5. Neighborhood enrichment ---
+    print("5. Generating neighborhood enrichment heatmap...")
+    try:
+        if 'leiden_nhood_enrichment' in adata.uns:
+            _plot_nhood_enrichment(adata, output_dir)
+        else:
+            print("   Skipping (no enrichment results found)")
+    except Exception as e:
+        print(f"   Error: {e}")
+
+    # --- 6. Co-occurrence ---
+    print("6. Generating co-occurrence plot...")
+    try:
+        if 'leiden_co_occurrence' in adata.uns:
+            _plot_co_occurrence(adata, output_dir)
+        else:
+            print("   Skipping (no co-occurrence results found)")
+    except Exception as e:
+        print(f"   Error: {e}")
+
+    # --- 7-8. SVG plots ---
+    svg_results = adata.uns.get('svg_results', None)
+    if svg_results is not None and len(svg_results) > 0:
+        print("7. Generating top SVGs bar plot...")
+        try:
+            _plot_top_svgs(svg_results, top_n_svgs, output_dir)
+        except Exception as e:
+            print(f"   Error: {e}")
+
+        print("8. Generating spatial plot of top SVG...")
+        try:
+            top_svg = svg_results.index[0]
+            if top_svg in adata.var_names:
+                _plot_spatial_svg(adata, top_svg, output_dir)
+            else:
+                print(f"   Skipping (top SVG '{top_svg}' not in var_names)")
+        except Exception as e:
+            print(f"   Error: {e}")
+    else:
+        print("7-8. Skipping SVG plots (no SVG results)")
+
+    print("\n" + "=" * 50)
+    print("✓ All visualizations generated successfully!")
+    print("=" * 50)