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
comparison
equal deleted inserted replaced
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,