opencode-knowledge-work 0.0.0-stage → 0.1.1

package/content/bio-research/skills/bio-research-scvi-tools/references/spatial_deconvolution.md

@@ -0,0 +1,438 @@
+# Spatial Transcriptomics Analysis
+
+This reference covers spatial transcriptomics analysis using scvi-tools methods: DestVI for deconvolution and resolVI for building spatial models.
+
+## Overview
+
+Spatial transcriptomics technologies like Visium capture gene expression at defined spatial locations, but many platforms have multi-cellular resolution. scvi-tools provides two main approaches:
+
+- **DestVI**: Deconvolution - estimates cell type proportions at each spot using a single-cell reference
+- **resolVI**: Builds a spatial model that learns gene expression patterns accounting for spatial context
+
+## Available Methods in scvi-tools
+
+| Method | Description | Use Case |
+|--------|-------------|----------|
+| **DestVI** | Variational inference for deconvolution | Estimate cell type proportions per spot |
+| **resolVI** | Spatial gene expression model | Learn spatially-aware representations |
+| **CondSCVI** | Reference model for DestVI | Required for DestVI workflow |
+
+## Prerequisites
+
+```python
+import scvi
+import scanpy as sc
+import squidpy as sq
+import numpy as np
+
+print(f"scvi-tools version: {scvi.__version__}")
+```
+
+---
+
+## Part 1: DestVI Deconvolution
+
+### Step 1: Load Spatial Data
+
+```python
+# Load Visium data
+adata_spatial = sc.read_visium("spaceranger_output/")
+
+# Check structure
+print(f"Spots: {adata_spatial.n_obs}")
+print(f"Genes: {adata_spatial.n_vars}")
+print(f"Spatial coordinates: {adata_spatial.obsm['spatial'].shape}")
+
+# Basic QC
+sc.pp.calculate_qc_metrics(adata_spatial, inplace=True)
+adata_spatial = adata_spatial[adata_spatial.obs['n_genes_by_counts'] > 200].copy()
+
+# Store counts
+adata_spatial.layers["counts"] = adata_spatial.X.copy()
+```
+
+### Step 2: Load Single-Cell Reference
+
+```python
+# Load reference single-cell data
+adata_sc = sc.read_h5ad("reference_scrna.h5ad")
+
+# Requirements:
+# - Raw counts
+# - Cell type annotations
+print(f"Reference cells: {adata_sc.n_obs}")
+print(f"Cell types: {adata_sc.obs['cell_type'].nunique()}")
+print(adata_sc.obs['cell_type'].value_counts())
+
+# Store counts
+adata_sc.layers["counts"] = adata_sc.X.copy()
+```
+
+### Step 3: Prepare Data
+
+```python
+# DestVI requires gene overlap between reference and spatial
+common_genes = adata_sc.var_names.intersection(adata_spatial.var_names)
+print(f"Common genes: {len(common_genes)}")
+
+adata_sc = adata_sc[:, common_genes].copy()
+adata_spatial = adata_spatial[:, common_genes].copy()
+```
+
+### Step 4: Train Reference Model (CondSCVI)
+
+```python
+# Train conditional scVI on reference data
+scvi.model.CondSCVI.setup_anndata(
+    adata_sc,
+    layer="counts",
+    labels_key="cell_type"
+)
+
+sc_model = scvi.model.CondSCVI(
+    adata_sc,
+    n_latent=20
+)
+
+sc_model.train(max_epochs=200)
+sc_model.history['elbo_train'].plot()
+```
+
+### Step 5: Train DestVI
+
+```python
+# Setup spatial data
+scvi.model.DestVI.setup_anndata(
+    adata_spatial,
+    layer="counts"
+)
+
+# Train DestVI using reference model
+spatial_model = scvi.model.DestVI.from_rna_model(
+    adata_spatial,
+    sc_model
+)
+
+spatial_model.train(max_epochs=500)
+```
+
+### Step 6: Get Cell Type Proportions
+
+```python
+# Infer cell type proportions at each spot
+proportions = spatial_model.get_proportions()
+
+# Add to adata
+for ct in adata_sc.obs['cell_type'].unique():
+    adata_spatial.obs[f'prop_{ct}'] = proportions[ct]
+
+# Visualize
+sq.pl.spatial_scatter(
+    adata_spatial,
+    color=[f'prop_{ct}' for ct in adata_sc.obs['cell_type'].unique()[:6]],
+    ncols=3
+)
+```
+
+---
+
+## Part 2: resolVI Spatial Model
+
+resolVI is a semi-supervised method that learns cell type assignments and spatially-aware representations directly from spatial data, optionally using initial cell type predictions.
+
+**Note**: resolVI is in `scvi.external` (not `scvi.model`).
+
+### Step 1: Prepare Spatial Data
+
+```python
+# Load and preprocess
+adata = sc.read_visium("spaceranger_output/")
+
+# QC
+sc.pp.calculate_qc_metrics(adata, inplace=True)
+adata = adata[adata.obs['n_genes_by_counts'] > 200].copy()
+
+# Store counts
+adata.layers["counts"] = adata.X.copy()
+
+# HVG selection
+sc.pp.highly_variable_genes(
+    adata,
+    n_top_genes=4000,
+    flavor="seurat_v3",
+    layer="counts"
+)
+adata = adata[:, adata.var['highly_variable']].copy()
+
+# Optional: Get initial cell type predictions (e.g., from a reference)
+# adata.obs["predicted_celltype"] = ...
+```
+
+### Step 2: Setup and Train resolVI
+
+```python
+# Setup for resolVI (note: scvi.external, not scvi.model)
+scvi.external.RESOLVI.setup_anndata(
+    adata,
+    labels_key="predicted_celltype",  # Initial cell type predictions
+    layer="counts"
+)
+
+# Create model (semisupervised=True uses the labels)
+model = scvi.external.RESOLVI(adata, semisupervised=True)
+
+# Train
+model.train(max_epochs=50)
+```
+
+### Step 3: Get Cell Type Predictions
+
+```python
+# Get refined cell type predictions
+# soft=True returns probabilities, soft=False returns labels
+cell_type_probs = model.predict(adata, num_samples=3, soft=True)
+cell_type_labels = model.predict(adata, num_samples=3, soft=False)
+
+adata.obs["resolvi_celltype"] = cell_type_labels
+
+# Visualize
+sq.pl.spatial_scatter(adata, color="resolvi_celltype")
+```
+
+### Step 4: Get Latent Representation
+
+```python
+# Get latent representation
+adata.obsm["X_resolVI"] = model.get_latent_representation(adata)
+
+# Cluster based on spatial representation
+sc.pp.neighbors(adata, use_rep="X_resolVI")
+sc.tl.umap(adata)
+sc.tl.leiden(adata, resolution=0.5)
+
+# Visualize clusters spatially
+sq.pl.spatial_scatter(adata, color="leiden")
+```
+
+### Step 5: Differential Expression
+
+```python
+# DE between cell types using resolVI
+de_results = model.differential_expression(
+    adata,
+    groupby="resolvi_celltype",
+    group1="T_cell",
+    group2="Tumor"
+)
+
+print(de_results.head(20))
+```
+
+### Step 6: Niche Abundance Analysis
+
+```python
+# Analyze how cell type neighborhoods differ between conditions
+# Requires spatial neighbor graph
+sq.gr.spatial_neighbors(adata, coord_type="generic")
+
+niche_results = model.differential_niche_abundance(
+    groupby="resolvi_celltype",
+    group1="T_cell",
+    group2="Tumor",
+    neighbor_key="spatial_neighbors"
+)
+```
+
+### Step 7: Query Mapping (Transfer to New Data)
+
+```python
+# Map new spatial data to trained model
+query_adata = sc.read_visium("new_sample/")
+query_adata.layers["counts"] = query_adata.X.copy()
+
+# Prepare and load query
+model.prepare_query_anndata(query_adata, reference_model=model)
+query_model = model.load_query_data(query_adata, reference_model=model)
+
+# Fine-tune on query
+query_model.train(max_epochs=20)
+
+# Get predictions for query
+query_labels = query_model.predict(query_adata, num_samples=3, soft=False)
+```
+
+---
+
+## Visualization
+
+### Spatial Proportions
+
+```python
+import matplotlib.pyplot as plt
+
+# Plot multiple cell type proportions
+cell_types = ['T_cell', 'Tumor', 'Fibroblast', 'Macrophage']
+fig, axes = plt.subplots(2, 2, figsize=(12, 12))
+
+for ax, ct in zip(axes.flat, cell_types):
+    sq.pl.spatial_scatter(
+        adata_spatial,
+        color=f'prop_{ct}',
+        ax=ax,
+        title=ct,
+        show=False
+    )
+
+plt.tight_layout()
+```
+
+### Enrichment by Region
+
+```python
+# Cluster spatial data
+sc.pp.neighbors(adata_spatial)
+sc.tl.leiden(adata_spatial, resolution=0.5)
+
+# Compare proportions across regions
+import pandas as pd
+
+cell_types = adata_sc.obs['cell_type'].unique()
+prop_cols = [f'prop_{ct}' for ct in cell_types]
+region_props = adata_spatial.obs.groupby('leiden')[prop_cols].mean()
+print(region_props)
+
+# Heatmap
+import seaborn as sns
+plt.figure(figsize=(10, 6))
+sns.heatmap(region_props.T, annot=True, cmap='viridis')
+plt.title('Cell Type Proportions by Region')
+```
+
+### Spatial Cell Type Interactions
+
+```python
+# Neighborhood enrichment using cell type assignments
+sq.gr.spatial_neighbors(adata_spatial)
+
+# Create "dominant cell type" annotation
+prop_cols = [f'prop_{ct}' for ct in cell_types]
+adata_spatial.obs['dominant_type'] = adata_spatial.obs[prop_cols].idxmax(axis=1)
+adata_spatial.obs['dominant_type'] = adata_spatial.obs['dominant_type'].str.replace('prop_', '')
+
+# Co-occurrence analysis
+sq.gr.co_occurrence(adata_spatial, cluster_key='dominant_type')
+sq.pl.co_occurrence(adata_spatial, cluster_key='dominant_type')
+```
+
+---
+
+## Complete DestVI Pipeline
+
+```python
+def deconvolve_spatial(
+    adata_spatial,
+    adata_ref,
+    cell_type_key="cell_type",
+    n_latent=20,
+    max_epochs_ref=200,
+    max_epochs_spatial=500
+):
+    """
+    Perform spatial deconvolution using DestVI.
+
+    Parameters
+    ----------
+    adata_spatial : AnnData
+        Spatial transcriptomics data
+    adata_ref : AnnData
+        Single-cell reference with cell type annotations
+    cell_type_key : str
+        Column in adata_ref.obs with cell type labels
+    n_latent : int
+        Latent dimensions
+    max_epochs_ref : int
+        Training epochs for reference model
+    max_epochs_spatial : int
+        Training epochs for spatial model
+
+    Returns
+    -------
+    AnnData with cell type proportions in obs
+    """
+    import scvi
+
+    # Get common genes
+    common_genes = adata_ref.var_names.intersection(adata_spatial.var_names)
+    adata_ref = adata_ref[:, common_genes].copy()
+    adata_spatial = adata_spatial[:, common_genes].copy()
+
+    # Ensure counts are stored
+    if "counts" not in adata_ref.layers:
+        adata_ref.layers["counts"] = adata_ref.X.copy()
+    if "counts" not in adata_spatial.layers:
+        adata_spatial.layers["counts"] = adata_spatial.X.copy()
+
+    # Train reference model
+    scvi.model.CondSCVI.setup_anndata(
+        adata_ref,
+        layer="counts",
+        labels_key=cell_type_key
+    )
+
+    ref_model = scvi.model.CondSCVI(adata_ref, n_latent=n_latent)
+    ref_model.train(max_epochs=max_epochs_ref)
+
+    # Train spatial model
+    scvi.model.DestVI.setup_anndata(adata_spatial, layer="counts")
+
+    spatial_model = scvi.model.DestVI.from_rna_model(
+        adata_spatial,
+        ref_model
+    )
+    spatial_model.train(max_epochs=max_epochs_spatial)
+
+    # Get proportions
+    proportions = spatial_model.get_proportions()
+
+    cell_types = adata_ref.obs[cell_type_key].unique()
+    for ct in cell_types:
+        adata_spatial.obs[f'prop_{ct}'] = proportions[ct]
+
+    # Add dominant type
+    prop_cols = [f'prop_{ct}' for ct in cell_types]
+    adata_spatial.obs['dominant_type'] = adata_spatial.obs[prop_cols].idxmax(axis=1)
+    adata_spatial.obs['dominant_type'] = adata_spatial.obs['dominant_type'].str.replace('prop_', '')
+
+    return adata_spatial, ref_model, spatial_model
+
+# Usage
+adata_spatial, ref_model, spatial_model = deconvolve_spatial(
+    adata_spatial,
+    adata_sc,
+    cell_type_key="cell_type"
+)
+
+# Visualize
+sq.pl.spatial_scatter(
+    adata_spatial,
+    color=['dominant_type', 'prop_T_cell', 'prop_Tumor'],
+    ncols=3
+)
+```
+
+---
+
+## Troubleshooting
+
+| Issue | Cause | Solution |
+|-------|-------|----------|
+| Few common genes | Different gene naming | Convert gene names (Ensembl ↔ Symbol) |
+| Poor deconvolution | Reference doesn't match | Use tissue-matched reference |
+| All spots same type | Over-smoothing | Adjust model parameters, check reference diversity |
+| NaN proportions | Missing cell types | Ensure all expected types in reference |
+| Training slow | Large spatial dataset | Reduce max_epochs, increase batch_size |
+
+## Key References
+
+- Lopez et al. (2022) "DestVI identifies continuums of cell types in spatial transcriptomics data"
+- [scvi-tools spatial tutorials](https://docs.scvi-tools.org/en/stable/tutorials/index.html)