Using RegVelo to predict perturbation#
Library imports#
import numpy as np
import pandas as pd
import scanpy as sc
from rgv_tools import DATA_DIR
from rgv_tools.perturbation import (
get_list_name,
Multiple_TFScanning,
split_elements,
TFScanning,
)
/home/icb/weixu.wang/miniconda3/envs/dynamo/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/dynamo/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/dynamo/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/dynamo/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/dynamo/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/dynamo/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/dynamo/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)
Constants#
DATASET = "zebrafish"
SAVE_DATA = True
if SAVE_DATA:
(DATA_DIR / DATASET / "results").mkdir(parents=True, exist_ok=True)
TERMINAL_STATES = [
"mNC_head_mesenchymal",
"mNC_arch2",
"mNC_hox34",
"Pigment",
]
single_ko = ["elk3", "erf", "fli1a", "mitfa", "nr2f5", "rarga", "rxraa", "smarcc1a", "tfec", "nr2f2"]
multiple_ko = ["fli1a_elk3", "mitfa_tfec", "tfec_mitfa_bhlhe40", "fli1a_erf_erfl3", "erf_erfl3"]
Data loading#
adata = sc.read_h5ad(DATA_DIR / DATASET / "processed" / "adata_preprocessed.h5ad")
Perturbation prediction#
Single gene knockout#
single_ko = set(single_ko).intersection(adata.var_names)
single_ko = list(single_ko)
for nrun in range(3):
model_name = "rgv_model_" + str(nrun)
coef_name = "coef_single_regvelo_" + str(nrun)
pval_name = "pval_single_regvelo_" + str(nrun)
model = DATA_DIR / DATASET / "processed" / "perturb_repeat_runs" / model_name
coef_save = DATA_DIR / DATASET / "results" / coef_name
pval_save = DATA_DIR / DATASET / "results" / pval_name
## Perturbation
d = TFScanning(model, adata, 8, "cell_type", TERMINAL_STATES, single_ko, 0)
coef = pd.DataFrame(np.array(d["coefficient"]))
coef.index = d["TF"]
coef.columns = get_list_name(d["coefficient"][0])
pval = pd.DataFrame(np.array(d["pvalue"]))
pval.index = d["TF"]
pval.columns = get_list_name(d["pvalue"][0])
coef = coef.loc[single_ko, :]
coef.to_csv(coef_save)
pval.to_csv(pval_save)
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 17:45:31,171 - INFO - Using pre-computed Schur decomposition
WARNING: Unable to import petsc4py. For installation, please refer to: https://petsc4py.readthedocs.io/en/stable/install.html.
Defaulting to `'gmres'` solver.
INFO File
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2024-11-24 17:45:41,723 - INFO - Using pre-computed Schur decomposition
Done elk3
INFO File
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WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 17:45:52,684 - INFO - Using pre-computed Schur decomposition
Done rxraa
INFO File
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2024-11-24 17:46:03,710 - INFO - Using pre-computed Schur decomposition
Done tfec
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WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 17:46:14,079 - INFO - Using pre-computed Schur decomposition
Done fli1a
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2024-11-24 17:46:24,385 - INFO - Using pre-computed Schur decomposition
Done nr2f5
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2024-11-24 17:46:34,948 - INFO - Using pre-computed Schur decomposition
Done rarga
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WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 17:46:45,238 - INFO - Using pre-computed Schur decomposition
Done nr2f2
INFO File
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2024-11-24 17:46:55,823 - INFO - Using pre-computed Schur decomposition
Done mitfa
INFO File
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WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 17:47:06,384 - INFO - Using pre-computed Schur decomposition
Done erf
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_1/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 17:47:17,183 - INFO - Using pre-computed Schur decomposition
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2024-11-24 17:47:27,667 - INFO - Using pre-computed Schur decomposition
Done elk3
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2024-11-24 17:47:38,381 - INFO - Using pre-computed Schur decomposition
Done rxraa
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2024-11-24 17:47:48,854 - INFO - Using pre-computed Schur decomposition
Done tfec
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2024-11-24 17:47:59,596 - INFO - Using pre-computed Schur decomposition
Done fli1a
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2024-11-24 17:48:10,572 - INFO - Using pre-computed Schur decomposition
Done nr2f5
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2024-11-24 17:48:21,079 - INFO - Using pre-computed Schur decomposition
Done rarga
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2024-11-24 17:48:31,622 - INFO - Using pre-computed Schur decomposition
Done nr2f2
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2024-11-24 17:48:42,238 - INFO - Using pre-computed Schur decomposition
Done mitfa
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el.pt already downloaded
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2024-11-24 17:48:53,001 - INFO - Using pre-computed Schur decomposition
Done erf
INFO File
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2024-11-24 17:49:03,680 - INFO - Using pre-computed Schur decomposition
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2024-11-24 17:49:14,410 - INFO - Using pre-computed Schur decomposition
Done elk3
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2024-11-24 17:49:25,247 - INFO - Using pre-computed Schur decomposition
Done rxraa
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2024-11-24 17:49:36,076 - INFO - Using pre-computed Schur decomposition
Done tfec
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2024-11-24 17:49:46,920 - INFO - Using pre-computed Schur decomposition
Done fli1a
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2024-11-24 17:49:58,372 - INFO - Using pre-computed Schur decomposition
Done nr2f5
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2024-11-24 17:50:09,453 - INFO - Using pre-computed Schur decomposition
Done rarga
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el.pt already downloaded
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2024-11-24 17:50:20,757 - INFO - Using pre-computed Schur decomposition
Done nr2f2
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el.pt already downloaded
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2024-11-24 17:50:32,045 - INFO - Using pre-computed Schur decomposition
Done mitfa
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_2/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 17:50:43,044 - INFO - Using pre-computed Schur decomposition
Done erf
Multiple knockout#
multiple_ko_list = split_elements(multiple_ko)
for nrun in [0, 1, 2]:
model_name = "rgv_model_" + str(nrun)
coef_name = "coef_multiple_regvelo_" + str(nrun)
pval_name = "pval_multiple_regvelo_" + str(nrun)
model = DATA_DIR / DATASET / "processed" / "perturb_repeat_runs" / model_name
coef_save = DATA_DIR / DATASET / "results" / coef_name
pval_save = DATA_DIR / DATASET / "results" / pval_name
## Perturbatiom
d = Multiple_TFScanning(model, adata, 8, "cell_type", TERMINAL_STATES, multiple_ko_list, 0)
coef = pd.DataFrame(np.array(d["coefficient"]))
coef.index = d["TF"]
coef.columns = get_list_name(d["coefficient"][0])
pval = pd.DataFrame(np.array(d["pvalue"]))
pval.index = d["TF"]
pval.columns = get_list_name(d["pvalue"][0])
coef.to_csv(coef_save)
pval.to_csv(pval_save)
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 17:50:54,421 - INFO - Using pre-computed Schur decomposition
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
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WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 17:51:05,483 - INFO - Using pre-computed Schur decomposition
Done fli1a_elk3
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2024-11-24 17:51:16,302 - INFO - Using pre-computed Schur decomposition
Done mitfa_tfec
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2024-11-24 17:51:26,882 - INFO - Using pre-computed Schur decomposition
Done tfec_mitfa_bhlhe40
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2024-11-24 17:51:37,651 - INFO - Using pre-computed Schur decomposition
Done fli1a_erf_erfl3
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2024-11-24 17:51:48,761 - INFO - Using pre-computed Schur decomposition
Done erf_erfl3
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2024-11-24 17:51:59,505 - INFO - Using pre-computed Schur decomposition
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2024-11-24 17:52:10,525 - INFO - Using pre-computed Schur decomposition
Done fli1a_elk3
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2024-11-24 17:52:21,320 - INFO - Using pre-computed Schur decomposition
Done mitfa_tfec
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el.pt already downloaded
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2024-11-24 17:52:32,526 - INFO - Using pre-computed Schur decomposition
Done tfec_mitfa_bhlhe40
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2024-11-24 17:52:43,786 - INFO - Using pre-computed Schur decomposition
Done fli1a_erf_erfl3
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2024-11-24 17:52:54,641 - INFO - Using pre-computed Schur decomposition
Done erf_erfl3
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2024-11-24 17:53:05,443 - INFO - Using pre-computed Schur decomposition
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2024-11-24 17:53:17,130 - INFO - Using pre-computed Schur decomposition
Done fli1a_elk3
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el.pt already downloaded
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2024-11-24 17:53:28,188 - INFO - Using pre-computed Schur decomposition
Done mitfa_tfec
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2024-11-24 17:53:39,255 - INFO - Using pre-computed Schur decomposition
Done tfec_mitfa_bhlhe40
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_2/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 17:53:50,234 - INFO - Using pre-computed Schur decomposition
Done fli1a_erf_erfl3
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_2/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 17:54:01,592 - INFO - Using pre-computed Schur decomposition
Done erf_erfl3