RegVelo-based analysis of hematopoiesis dataset

Contents

RegVelo-based analysis of hematopoiesis dataset#

Notebook runs the RegVelo model on the hematopoiesis dataset without any regularization.

Library imports#

import numpy as np
import torch

import anndata as ad
import scanpy as sc
import scvi
from regvelo import REGVELOVI

from rgv_tools import DATA_DIR
from rgv_tools.benchmarking import set_output

/home/icb/weixu.wang/miniconda3/envs/regvelo_test/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_csv from `anndata` is deprecated. Import anndata.io.read_csv instead.
  warnings.warn(msg, FutureWarning)
/home/icb/weixu.wang/miniconda3/envs/regvelo_test/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_excel from `anndata` is deprecated. Import anndata.io.read_excel instead.
  warnings.warn(msg, FutureWarning)
/home/icb/weixu.wang/miniconda3/envs/regvelo_test/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_hdf from `anndata` is deprecated. Import anndata.io.read_hdf instead.
  warnings.warn(msg, FutureWarning)
/home/icb/weixu.wang/miniconda3/envs/regvelo_test/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_loom from `anndata` is deprecated. Import anndata.io.read_loom instead.
  warnings.warn(msg, FutureWarning)
/home/icb/weixu.wang/miniconda3/envs/regvelo_test/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_mtx from `anndata` is deprecated. Import anndata.io.read_mtx instead.
  warnings.warn(msg, FutureWarning)
/home/icb/weixu.wang/miniconda3/envs/regvelo_test/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_text from `anndata` is deprecated. Import anndata.io.read_text instead.
  warnings.warn(msg, FutureWarning)
/home/icb/weixu.wang/miniconda3/envs/regvelo_test/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_umi_tools from `anndata` is deprecated. Import anndata.io.read_umi_tools instead.
  warnings.warn(msg, FutureWarning)
/home/icb/weixu.wang/miniconda3/envs/regvelo_test/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_csv from `anndata` is deprecated. Import anndata.io.read_csv instead.
  warnings.warn(msg, FutureWarning)
/home/icb/weixu.wang/miniconda3/envs/regvelo_test/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_loom from `anndata` is deprecated. Import anndata.io.read_loom instead.
  warnings.warn(msg, FutureWarning)
/home/icb/weixu.wang/miniconda3/envs/regvelo_test/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_text from `anndata` is deprecated. Import anndata.io.read_text instead.
  warnings.warn(msg, FutureWarning)
/home/icb/weixu.wang/miniconda3/envs/regvelo_test/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing CSCDataset from `anndata.experimental` is deprecated. Import anndata.abc.CSCDataset instead.
  warnings.warn(msg, FutureWarning)
/home/icb/weixu.wang/miniconda3/envs/regvelo_test/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing CSRDataset from `anndata.experimental` is deprecated. Import anndata.abc.CSRDataset instead.
  warnings.warn(msg, FutureWarning)
/home/icb/weixu.wang/miniconda3/envs/regvelo_test/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_elem from `anndata.experimental` is deprecated. Import anndata.io.read_elem instead.
  warnings.warn(msg, FutureWarning)

General settings#

scvi.settings.seed = 0

[rank: 0] Seed set to 0

Constants#

DATASET = "hematopoiesis"

SAVE_DATA = True
if SAVE_DATA:
    (DATA_DIR / DATASET / "processed").mkdir(parents=True, exist_ok=True)

Data loading#

adata = ad.io.read_h5ad(DATA_DIR / DATASET / "processed" / "adata_preprocessed.h5ad")

Run RegVelo#

## prepare skeleton
skeleton = adata.uns["skeleton"].copy()
skeleton = torch.tensor(np.array(skeleton)).int()

## prepare TF
tfs = adata.var_names[adata.var["tf"]]

## prepare model
REGVELOVI.setup_anndata(adata, spliced_layer="Ms", unspliced_layer="Mu")
vae = REGVELOVI(adata, W=skeleton.T, regulators=tfs)

vae.train()

/home/icb/weixu.wang/miniconda3/envs/regvelo_test/lib/python3.10/site-packages/lightning/fabric/plugins/environments/slurm.py:204: The `srun` command is available on your system but is not used. HINT: If your intention is to run Lightning on SLURM, prepend your python command with `srun` like so: srun python /home/icb/weixu.wang/miniconda3/envs/regvelo_test/li ...
/home/icb/weixu.wang/miniconda3/envs/regvelo_test/lib/python3.10/site-packages/lightning/fabric/plugins/environments/slurm.py:204: The `srun` command is available on your system but is not used. HINT: If your intention is to run Lightning on SLURM, prepend your python command with `srun` like so: srun python /home/icb/weixu.wang/miniconda3/envs/regvelo_test/li ...
GPU available: True (cuda), used: True
TPU available: False, using: 0 TPU cores
HPU available: False, using: 0 HPUs
/home/icb/weixu.wang/miniconda3/envs/regvelo_test/lib/python3.10/site-packages/lightning/fabric/plugins/environments/slurm.py:204: The `srun` command is available on your system but is not used. HINT: If your intention is to run Lightning on SLURM, prepend your python command with `srun` like so: srun python /home/icb/weixu.wang/miniconda3/envs/regvelo_test/li ...
LOCAL_RANK: 0 - CUDA_VISIBLE_DEVICES: [0]
/home/icb/weixu.wang/miniconda3/envs/regvelo_test/lib/python3.10/site-packages/lightning/pytorch/trainer/connectors/data_connector.py:424: The 'train_dataloader' does not have many workers which may be a bottleneck. Consider increasing the value of the `num_workers` argument` to `num_workers=5` in the `DataLoader` to improve performance.
/home/icb/weixu.wang/miniconda3/envs/regvelo_test/lib/python3.10/site-packages/lightning/pytorch/loops/fit_loop.py:298: The number of training batches (1) is smaller than the logging interval Trainer(log_every_n_steps=10). Set a lower value for log_every_n_steps if you want to see logs for the training epoch.
/home/icb/weixu.wang/miniconda3/envs/regvelo_test/lib/python3.10/site-packages/lightning/pytorch/trainer/connectors/data_connector.py:424: The 'val_dataloader' does not have many workers which may be a bottleneck. Consider increasing the value of the `num_workers` argument` to `num_workers=5` in the `DataLoader` to improve performance.

Monitored metric elbo_validation did not improve in the last 45 records. Best score: -362.692. Signaling Trainer to stop.

set_output(adata, vae, n_samples=30, batch_size=adata.n_obs)

Save dataset#

Recalculate the PCA downstream CBC calculation because velocity is calculated from the moment matrices

sc.tl.pca(adata, layer="Ms")

Save adata with velocity layer

if SAVE_DATA:
    adata.write_h5ad(DATA_DIR / DATASET / "processed" / "adata_run_regvelo_unregularized.h5ad")