Mercurial > repos > ebi-gxa > decoupler_pathway_inference
comparison decoupler_pseudobulk.py @ 4:6c30272fb587 draft
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 54818daabaf1251642a267e5766f13741cb7faeb
| author | ebi-gxa |
|---|---|
| date | Sun, 15 Sep 2024 09:56:39 +0000 |
| parents | c6787c2aee46 |
| children | 87f1eaa410cc |
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| 3:c6787c2aee46 | 4:6c30272fb587 |
|---|---|
| 318 use_raw=args.use_raw, | 318 use_raw=args.use_raw, |
| 319 min_cells=args.min_cells, | 319 min_cells=args.min_cells, |
| 320 min_counts=args.min_counts, | 320 min_counts=args.min_counts, |
| 321 ) | 321 ) |
| 322 | 322 |
| 323 print("Created pseudo-bulk AnnData, checking if fields still make sense.") | |
| 324 print( | |
| 325 "If this fails this check, it might mean that you asked for factors " | |
| 326 + "that are not compatible with you sample identifiers (ie. asked for " | |
| 327 + "phase in the factors, but each sample contains more than one phase, " | |
| 328 + "try joining fields)" | |
| 329 ) | |
| 330 if factor_fields: | |
| 331 check_fields( | |
| 332 factor_fields, | |
| 333 pseudobulk_data, | |
| 334 context=" after creation of pseudo-bulk AnnData", | |
| 335 ) | |
| 336 print("Factors requested are adequate for the pseudo-bulked AnnData!") | |
| 337 | |
| 323 # Plot pseudobulk samples | 338 # Plot pseudobulk samples |
| 324 plot_pseudobulk_samples( | 339 plot_pseudobulk_samples( |
| 325 pseudobulk_data, | 340 pseudobulk_data, |
| 326 args.groupby, | 341 args.groupby, |
| 327 save_path=args.save_path, | 342 save_path=args.save_path, |