| import anndata | |
| import numpy as np | |
| uce = anndata.read_h5ad("data/tahoe_universal_embeddings.h5ad") | |
| control_condition = "[('DMSO_TF', 0.0, 'uM')]" | |
| X_delta = np.zeros_like(uce.obsm["X_uce"]) | |
| for cell_line in uce.obs["cell_line"].unique(): | |
| for plate in uce.obs["plate"].unique(): | |
| cell_plate_mask = (uce.obs["cell_line"] == cell_line) & (uce.obs["plate"] == plate) | |
| control_mask = cell_plate_mask & (uce.obs["drugname_drugconc"] == control_condition) | |
| cell_plate_indices = np.where(cell_plate_mask)[0] | |
| control_indices = np.where(control_mask)[0] | |
| X_delta[cell_plate_indices] = uce.obsm["X_uce"][cell_plate_indices] - uce.obsm["X_uce"][control_indices] | |
| uce.obsm["X_delta"] = X_delta | |
| print("X_uce shape", uce.obsm["X_uce"].shape) | |
| print("X_delta shape", uce.obsm["X_delta"].shape) | |
| uce.write("data/tahoe_universal_embeddings_deltas.h5ad") |