Multiome Analysis with MultiVI

This reference covers joint RNA and ATAC-seq analysis from multiome experiments using MultiVI.

Overview

MultiVI is a deep generative model for analyzing multiome data (simultaneous RNA-seq and ATAC-seq from the same cells). It:

• Learns a joint latent representation across modalities
• Handles missing modalities (RNA-only or ATAC-only cells)
• Enables batch correction across experiments
• Supports imputation of missing modalities

Prerequisites

import scvi
import scanpy as sc
import mudata as md
import numpy as np

print(f"scvi-tools version: {scvi.__version__}")

Data Formats

Option 1: MuData (Recommended)

# Load multiome data as MuData
mdata = md.read("multiome.h5mu")

# Structure:
# mdata.mod['rna']  - AnnData with RNA counts
# mdata.mod['atac'] - AnnData with ATAC counts

print(f"RNA: {mdata.mod['rna'].shape}")
print(f"ATAC: {mdata.mod['atac'].shape}")

Option 2: Separate AnnData Objects

# Load separately
adata_rna = sc.read_h5ad("rna.h5ad")
adata_atac = sc.read_h5ad("atac.h5ad")

# Ensure same cells in same order
common_cells = adata_rna.obs_names.intersection(adata_atac.obs_names)
adata_rna = adata_rna[common_cells].copy()
adata_atac = adata_atac[common_cells].copy()

Step 1: Prepare RNA Data

# RNA preprocessing (standard scvi-tools pipeline)
adata_rna = mdata.mod['rna'].copy()

# Filter
sc.pp.filter_cells(adata_rna, min_genes=200)
sc.pp.filter_genes(adata_rna, min_cells=3)

# Store counts
adata_rna.layers["counts"] = adata_rna.X.copy()

# HVG selection
sc.pp.highly_variable_genes(
    adata_rna,
    n_top_genes=4000,
    flavor="seurat_v3",
    layer="counts",
    batch_key="batch"  # If multiple batches
)

# Subset to HVGs
adata_rna = adata_rna[:, adata_rna.var['highly_variable']].copy()

Step 2: Prepare ATAC Data

# ATAC preprocessing
adata_atac = mdata.mod['atac'].copy()

# Filter peaks
sc.pp.filter_genes(adata_atac, min_cells=10)

# Binarize accessibility
adata_atac.X = (adata_atac.X > 0).astype(np.float32)

# Select top accessible peaks (if too many)
if adata_atac.n_vars > 50000:
    peak_accessibility = np.array(adata_atac.X.sum(axis=0)).flatten()
    top_peaks = np.argsort(peak_accessibility)[-50000:]
    adata_atac = adata_atac[:, top_peaks].copy()

# Store in layer
adata_atac.layers["counts"] = adata_atac.X.copy()

Step 3: Create Combined MuData

# Ensure matching cells
common_cells = adata_rna.obs_names.intersection(adata_atac.obs_names)
adata_rna = adata_rna[common_cells].copy()
adata_atac = adata_atac[common_cells].copy()

# Create MuData
mdata = md.MuData({
    "rna": adata_rna,
    "atac": adata_atac
})

print(f"Combined multiome: {mdata.n_obs} cells")
print(f"RNA features: {mdata.mod['rna'].n_vars}")
print(f"ATAC features: {mdata.mod['atac'].n_vars}")

Step 4: Setup MultiVI

# Setup MuData for MultiVI
scvi.model.MULTIVI.setup_mudata(
    mdata,
    rna_layer="counts",
    atac_layer="counts",
    batch_key="batch",  # Optional
    modalities={
        "rna_layer": "rna",
        "batch_key": "rna",
        "atac_layer": "atac"
    }
)

Step 5: Train MultiVI

# Create model
model = scvi.model.MULTIVI(
    mdata,
    n_latent=20,
    n_layers_encoder=2,
    n_layers_decoder=2
)

# Train
model.train(
    max_epochs=300,
    early_stopping=True,
    early_stopping_patience=10,
    batch_size=128
)

# Check training
model.history['elbo_train'].plot()

Step 6: Get Joint Representation

# Latent representation
latent = model.get_latent_representation()

# Add to MuData
mdata.obsm["X_MultiVI"] = latent

# Clustering on joint space
sc.pp.neighbors(mdata, use_rep="X_MultiVI")
sc.tl.umap(mdata)
sc.tl.leiden(mdata, resolution=1.0)

# Visualize
sc.pl.umap(mdata, color=['leiden', 'batch'], ncols=2)

Step 7: Modality-Specific Analysis

Impute Missing Modality

# Impute RNA expression for ATAC-only cells
# (Useful when integrating with ATAC-only datasets)
imputed_rna = model.get_normalized_expression(
    modality="rna"
)

# Impute accessibility for RNA-only cells
imputed_atac = model.get_accessibility_estimates()

Differential Analysis

# Differential expression (RNA)
de_results = model.differential_expression(
    groupby="leiden",
    group1="0",
    group2="1"
)

# Differential accessibility (ATAC)
da_results = model.differential_accessibility(
    groupby="leiden",
    group1="0",
    group2="1"
)

Handling Partial Data

MultiVI can integrate datasets with only one modality:

# Dataset 1: Full multiome
# Dataset 2: RNA only
# Dataset 3: ATAC only

# Mark missing modalities
mdata.obs['modality'] = 'paired'  # For cells with both
# For RNA-only cells, ATAC data should be missing/NaN
# For ATAC-only cells, RNA data should be missing/NaN

# MultiVI handles this automatically during training

Complete Pipeline

def analyze_multiome(
    adata_rna,
    adata_atac,
    batch_key=None,
    n_top_genes=4000,
    n_top_peaks=50000,
    n_latent=20,
    max_epochs=300
):
    """
    Complete multiome analysis with MultiVI.

    Parameters
    ----------
    adata_rna : AnnData
        RNA count data
    adata_atac : AnnData
        ATAC peak data
    batch_key : str, optional
        Batch column name
    n_top_genes : int
        Number of HVGs for RNA
    n_top_peaks : int
        Number of top peaks for ATAC
    n_latent : int
        Latent dimensions
    max_epochs : int
        Maximum training epochs

    Returns
    -------
    MuData with joint representation
    """
    import scvi
    import scanpy as sc
    import mudata as md
    import numpy as np

    # Get common cells
    common_cells = adata_rna.obs_names.intersection(adata_atac.obs_names)
    adata_rna = adata_rna[common_cells].copy()
    adata_atac = adata_atac[common_cells].copy()

    # RNA preprocessing
    sc.pp.filter_genes(adata_rna, min_cells=3)
    adata_rna.layers["counts"] = adata_rna.X.copy()

    if batch_key:
        sc.pp.highly_variable_genes(
            adata_rna, n_top_genes=n_top_genes,
            flavor="seurat_v3", layer="counts", batch_key=batch_key
        )
    else:
        sc.pp.normalize_total(adata_rna, target_sum=1e4)
        sc.pp.log1p(adata_rna)
        sc.pp.highly_variable_genes(adata_rna, n_top_genes=n_top_genes)
        adata_rna.X = adata_rna.layers["counts"].copy()

    adata_rna = adata_rna[:, adata_rna.var['highly_variable']].copy()

    # ATAC preprocessing
    sc.pp.filter_genes(adata_atac, min_cells=10)
    adata_atac.X = (adata_atac.X > 0).astype(np.float32)

    if adata_atac.n_vars > n_top_peaks:
        peak_acc = np.array(adata_atac.X.sum(axis=0)).flatten()
        top_idx = np.argsort(peak_acc)[-n_top_peaks:]
        adata_atac = adata_atac[:, top_idx].copy()

    adata_atac.layers["counts"] = adata_atac.X.copy()

    # Create MuData
    mdata = md.MuData({"rna": adata_rna, "atac": adata_atac})

    # Setup and train
    scvi.model.MULTIVI.setup_mudata(
        mdata,
        rna_layer="counts",
        atac_layer="counts",
        batch_key=batch_key,
        modalities={"rna_layer": "rna", "batch_key": "rna", "atac_layer": "atac"}
    )

    model = scvi.model.MULTIVI(mdata, n_latent=n_latent)
    model.train(max_epochs=max_epochs, early_stopping=True)

    # Add representation
    mdata.obsm["X_MultiVI"] = model.get_latent_representation()

    # Cluster
    sc.pp.neighbors(mdata, use_rep="X_MultiVI")
    sc.tl.umap(mdata)
    sc.tl.leiden(mdata)

    return mdata, model


# Usage
mdata, model = analyze_multiome(
    adata_rna,
    adata_atac,
    batch_key="sample"
)

sc.pl.umap(mdata, color=['leiden', 'sample'])

Peak-to-Gene Linking

# Link ATAC peaks to genes based on correlation in latent space
# This identifies regulatory relationships

def link_peaks_to_genes(model, mdata, distance_threshold=100000):
    """
    Link peaks to nearby genes based on correlation.

    Parameters
    ----------
    model : MULTIVI
        Trained model
    mdata : MuData
        Multiome data
    distance_threshold : int
        Maximum distance (bp) to link peak to gene

    Returns
    -------
    DataFrame of peak-gene links
    """
    # Get imputed values
    rna_imputed = model.get_normalized_expression()
    atac_imputed = model.get_accessibility_estimates()

    # Correlate peak accessibility with gene expression
    # for peaks near gene promoters
    # ... (requires genomic coordinates)

    return peak_gene_links

Troubleshooting

Key References

• Ashuach et al. (2023) "MultiVI: deep generative model for the integration of multimodal data"