Bio Spatial Transcriptomics Spatial Domains

import squidpy as sq
import scanpy as sc
import numpy as np
import matplotlib.pyplot as plt

Standard Clustering (Expression Only)

Goal: Cluster spots based purely on gene expression, ignoring spatial location.

Approach: Build an expression-based neighbor graph, then apply Leiden community detection.

# Standard Leiden clustering (ignores spatial context)
sc.pp.neighbors(adata, n_neighbors=15, n_pcs=30)
sc.tl.leiden(adata, resolution=0.5, key_added='leiden')

# Visualize on tissue
sq.pl.spatial_scatter(adata, color='leiden', size=1.3)

Spatial-Aware Clustering with Squidpy

Goal: Cluster spots using only spatial proximity to identify contiguous tissue regions.

Approach: Build a spatial neighbor graph, then run Leiden clustering on the spatial graph.

# Build spatial neighbors
sq.gr.spatial_neighbors(adata, coord_type='generic', n_neighs=6)

# Run Leiden on spatial graph
sc.tl.leiden(adata, resolution=0.5, key_added='spatial_leiden', neighbors_key='spatial_neighbors')

sq.pl.spatial_scatter(adata, color='spatial_leiden', size=1.3)

Combined Expression + Spatial Graph

Goal: Integrate both expression similarity and spatial proximity for domain detection.

Approach: Build separate expression and spatial graphs, normalize each, then combine as a weighted average for clustering.

from scipy.sparse import csr_matrix
from sklearn.preprocessing import normalize

# Build both graphs
sq.gr.spatial_neighbors(adata, coord_type='generic', n_neighs=6)
sc.pp.neighbors(adata, n_neighbors=15, n_pcs=30)

# Combine graphs (weighted average)
spatial_weight = 0.3
spatial_conn = adata.obsp['spatial_connectivities']
expr_conn = adata.obsp['connectivities']

# Normalize
spatial_norm = normalize(spatial_conn, norm='l1', axis=1)
expr_norm = normalize(expr_conn, norm='l1', axis=1)

# Combine
combined = spatial_weight * spatial_norm + (1 - spatial_weight) * expr_norm
adata.obsp['combined_connectivities'] = csr_matrix(combined)

# Cluster on combined graph
sc.tl.leiden(adata, resolution=0.5, key_added='combined_leiden', adjacency=adata.obsp['combined_connectivities'])

BayesSpace (R Integration)

# BayesSpace provides spatial smoothing for domain detection
# Run in R, then import results

# R code (run separately):
# library(BayesSpace)
# sce <- readRDS("sce.rds")
# sce <- spatialPreprocess(sce, platform="Visium")
# sce <- spatialCluster(sce, q=7, nrep=10000)
# saveRDS(sce, "sce_bayesspace.rds")

# Import BayesSpace results
import rpy2.robjects as ro
from rpy2.robjects import pandas2ri
pandas2ri.activate()

ro.r('sce <- readRDS("sce_bayesspace.rds")')
spatial_clusters = ro.r('colData(sce)$spatial.cluster')
adata.obs['bayesspace'] = list(spatial_clusters)

STAGATE for Spatial Domains

Goal: Detect spatial domains using deep learning with graph attention networks.

Approach: Build a spatial graph with STAGATE, train the model to learn spatially-aware embeddings, then cluster on those embeddings.

# STAGATE uses graph attention for spatial domain detection
import STAGATE

# Build graph
STAGATE.Cal_Spatial_Net(adata, rad_cutoff=150)
STAGATE.Stats_Spatial_Net(adata)

# Train STAGATE
adata = STAGATE.train_STAGATE(adata, alpha=0)

# Cluster on STAGATE embeddings
sc.pp.neighbors(adata, use_rep='STAGATE')
sc.tl.leiden(adata, resolution=0.5, key_added='stagate_leiden')

Evaluate Domain Quality

Goal: Assess whether identified domains form spatially and transcriptionally coherent regions.

Approach: Compute silhouette scores separately for spatial coordinates and expression PCA to quantify domain separation.

# Check if domains are spatially coherent
from sklearn.metrics import silhouette_score

coords = adata.obsm['spatial']
labels = adata.obs['spatial_leiden'].values

# Spatial silhouette score
spatial_silhouette = silhouette_score(coords, labels)
print(f'Spatial silhouette score: {spatial_silhouette:.3f}')

# Expression silhouette score
expr_silhouette = silhouette_score(adata.obsm['X_pca'], labels)
print(f'Expression silhouette score: {expr_silhouette:.3f}')

Refine Domain Boundaries

Goal: Smooth noisy domain assignments to produce cleaner spatial boundaries.

Approach: Apply iterative majority-vote smoothing using the spatial neighbor graph to reassign each spot to the most common label among its neighbors.

# Smooth domain assignments using spatial neighbors
from scipy import sparse

def smooth_domains(adata, cluster_key, n_iter=1):
    conn = adata.obsp['spatial_connectivities']
    labels = adata.obs[cluster_key].values
    categories = adata.obs[cluster_key].cat.categories

    for _ in range(n_iter):
        new_labels = []
        for i in range(adata.n_obs):
            neighbors = conn[i].nonzero()[1]
            if len(neighbors) > 0:
                neighbor_labels = labels[neighbors]
                # Majority vote
                unique, counts = np.unique(neighbor_labels, return_counts=True)
                new_labels.append(unique[counts.argmax()])
            else:
                new_labels.append(labels[i])
        labels = np.array(new_labels)

    adata.obs[f'{cluster_key}_smoothed'] = pd.Categorical(labels, categories=categories)

smooth_domains(adata, 'leiden', n_iter=2)
sq.pl.spatial_scatter(adata, color=['leiden', 'leiden_smoothed'], ncols=2)

Compare Domain Methods

# Compare different clustering approaches
from sklearn.metrics import adjusted_rand_score

methods = ['leiden', 'spatial_leiden', 'combined_leiden']
for i, m1 in enumerate(methods):
    for m2 in methods[i+1:]:
        ari = adjusted_rand_score(adata.obs[m1], adata.obs[m2])
        print(f'{m1} vs {m2}: ARI = {ari:.3f}')

Domain Markers

Goal: Identify marker genes that distinguish each spatial domain from the rest.

Approach: Run Wilcoxon rank-sum tests per domain, then extract and visualize top-ranked differentially expressed genes.

# Find marker genes for each domain
sc.tl.rank_genes_groups(adata, groupby='spatial_leiden', method='wilcoxon')

# Get top markers
markers = sc.get.rank_genes_groups_df(adata, group=None)
print(markers.groupby('group').head(5))

# Plot top markers on tissue
top_markers = markers.groupby('group').head(1)['names'].tolist()
sq.pl.spatial_scatter(adata, color=top_markers[:6], ncols=3)

Annotate Domains

Goal: Assign biological labels to spatial domain clusters based on marker gene identity.

Approach: Map cluster IDs to anatomical region names using a dictionary and visualize the annotated tissue.

# Manual annotation based on markers
domain_annotations = {
    '0': 'White matter',
    '1': 'Cortex layer 1',
    '2': 'Cortex layer 2/3',
    '3': 'Cortex layer 4',
    '4': 'Cortex layer 5',
    '5': 'Cortex layer 6',
}

adata.obs['domain'] = adata.obs['spatial_leiden'].map(domain_annotations)
sq.pl.spatial_scatter(adata, color='domain', size=1.3)

Related Skills

• spatial-neighbors - Build spatial graphs (prerequisite)
• spatial-statistics - Compute spatial statistics per domain
• single-cell/clustering - Standard clustering methods