Mercurial > repos > ebi-gxa > decoupler_pathway_inference
comparison decoupler_pseudobulk.py @ 12:4523224b53ce draft default tip
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 626c1018b662202de10ce77f123fc27f584beb9c
| author | ebi-gxa |
|---|---|
| date | Fri, 13 Jun 2025 09:08:13 +0000 |
| parents | db14ac3f6b43 |
| children |
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| 11:db14ac3f6b43 | 12:4523224b53ce |
|---|---|
| 322 >>> import scanpy as sc | 322 >>> import scanpy as sc |
| 323 >>> adata = sc.datasets.pbmc68k_reduced() | 323 >>> adata = sc.datasets.pbmc68k_reduced() |
| 324 >>> check_fields(["bulk_labels", "louvain"], adata, obs=True) | 324 >>> check_fields(["bulk_labels", "louvain"], adata, obs=True) |
| 325 """ | 325 """ |
| 326 | 326 |
| 327 # Fields that will be created during the pseudobulking process | |
| 328 pseudobulk_generated_fields = ['psbulk_n_cells', 'psbulk_counts'] | |
| 329 | |
| 330 # Filter out the pseudobulk-generated fields from checking | |
| 331 fields_to_check = [field for field in fields | |
| 332 if field not in pseudobulk_generated_fields] | |
| 333 | |
| 327 legend = "" | 334 legend = "" |
| 328 if context: | 335 if context: |
| 329 legend = f", passed in {context}," | 336 legend = f", passed in {context}," |
| 330 if obs: | 337 if obs: |
| 331 if not set(fields).issubset(set(adata.obs.columns)): | 338 if not set(fields_to_check).issubset(set(adata.obs.columns)): |
| 332 raise ValueError( | 339 raise ValueError( |
| 333 f"Some of the following fields {legend} are not present \ | 340 f"Some of the following fields {legend} are not present \ |
| 334 in adata.obs: {fields}. \ | 341 in adata.obs: {fields_to_check}. \ |
| 335 Possible fields are: {list(set(adata.obs.columns))}" | 342 Possible fields are: {list(set(adata.obs.columns))}" |
| 336 ) | 343 ) |
| 337 else: | 344 else: |
| 338 if not set(fields).issubset(set(adata.var.columns)): | 345 if not set(fields_to_check).issubset(set(adata.var.columns)): |
| 339 raise ValueError( | 346 raise ValueError( |
| 340 f"Some of the following fields {legend} are not present \ | 347 f"Some of the following fields {legend} are not present \ |
| 341 in adata.var: {fields}. \ | 348 in adata.var: {fields_to_check}. \ |
| 342 Possible fields are: {list(set(adata.var.columns))}" | 349 Possible fields are: {list(set(adata.var.columns))}" |
| 343 ) | 350 ) |
| 344 | 351 |
| 345 | 352 |
| 346 def main(args): | 353 def main(args): |