BulkTrajBlend trajectory interpolation
Overview
Invoke this skill when users need to bridge gaps in single-cell developmental trajectories using matched bulk RNA-seq. It follows t_bulktrajblend.ipynb, showcasing how BulkTrajBlend deconvolves PDAC bulk samples, identifies overlapping communities with a GNN, and interpolates "interrupted" cell states.
Instructions
- Prepare libraries and inputs
- Import omicverse as ov, scanpy as sc, scvelo as scv, and helper functions like from omicverse.utils import mde; run ov.plot_set(). - Load the reference scRNA-seq AnnData (scv.datasets.dentategyrus()) and raw bulk counts with ov.utils.read(...) followed by ov.bulk.Matrix_ID_mapping(...) for gene ID harmonisation.
- Configure BulkTrajBlend
- Instantiate ov.bulk2single.BulkTrajBlend(bulk_seq=bulk_df, single_seq=adata, bulk_group=['dg_d_1','dg_d_2','dg_d_3'], celltype_key='clusters'). - Explain that bulk_group names correspond to raw bulk columns and the method expects unscaled counts.
- Set beta-VAE expectations
- Call bulktb.vae_configure(cell_target_num=100) (or pass a dictionary) to define expected cell counts per cluster. Mention that omitting the argument triggers TAPE-based estimation.
- Train or load the beta-VAE
- Use bulktb.vae_train(batch_size=512, learning_rate=1e-4, hidden_size=256, epoch_num=3500, vae_save_dir='...', vae_save_name='dg_btb_vae', generate_save_dir='...', generate_save_name='dg_btb'). - Highlight resuming with bulktb.vae_load('.../dg_btb_vae.pth') and the need to regenerate cells with consistent random seeds for reproducibility.
- Generate synthetic cells
- Produce filtered AnnData via bulktb.vae_generate(leiden_size=25) and inspect compositions with ov.bulk2single.bulk2single_plot_cellprop(...). - Save outputs to disk for reuse (adata.write_h5ad).
- Configure and train the GNN
- Call bulktb.gnn_configure(max_epochs=2000, use_rep='X', neighbor_rep='X_pca', gpu=0,...) to set hyperparameters. - Train using bulktb.gnn_train(); reload checkpoints with bulktb.gnn_load('save_model/gnn.pth'). - Generate overlapping community assignments through bulktb.gnn_generate().
- Visualise community structure
- Create MDE embeddings: bulktb.nocd_obj.adata.obsm['X_mde'] = mde(bulktb.nocd_obj.adata.obsm['X_pca']). - Plot clusters vs. discovered communities using sc.pl.embedding(..., color=['clusters','nocd_n'], palette=ov.utils.pyomic_palette()) and filtered subsets excluding synthetic labels with hyphens.
- Interpolate missing states
- Run bulktb.interpolation('OPC') (replace with target lineage) to synthesise continuity, then preprocess the interpolated AnnData (HVG selection, scaling, PCA). - Compute embeddings with mde, visualise with ov.pl.embedding, and compare to the original atlas.
- Analyse trajectories
- Initialise ov.single.pyVIA on both original and interpolated data to derive pseudotime, followed by get_pseudotime, ov.pp.neighbors, ov.utils.cal_paga, and ov.utils.plot_paga for topology validation.
- Defensive validation
# Before BulkTrajBlend: verify bulk_group columns exist for g in bulk_group: assert g in bulk_df.columns, f"Bulk group '{g}' not in bulk data columns" # Verify celltype_key exists in reference assert celltype_key in adata.obs.columns, f"Cell type column '{celltype_key}' not in reference AnnData" # Verify gene name overlap shared = set(bulk_df.index) & set(adata.var_names) assert len(shared) > 100, f"Only {len(shared)} shared genes — harmonize gene IDs first" - Troubleshooting tips
- If the VAE collapses (high reconstruction loss), lower learning_rate or reduce hidden_size. - Ensure the same generated dataset is used before calling gnn_train; regenerating cells changes the graph and can break checkpoint loading. - Sparse clusters may need adjusted cell_target_num thresholds or a smaller leiden_size filter to retain rare populations.
Examples
- "Train BulkTrajBlend on PDAC cohorts, then interpolate missing OPC states in the trajectory."
- "Load saved beta-VAE and GNN weights to regenerate overlapping communities and plot cluster vs. nocd labels."
- "Run VIA on interpolated cells and compare PAGA graphs with the original scRNA-seq trajectory."
References
- Tutorial notebook:
t_bulktrajblend.ipynb - Example datasets and checkpoints:
omicverse_guide/docs/Tutorials-bulk2single/data/ - Quick copy/paste commands:
reference.md