Mercurial > repos > ebi-gxa > decoupler_pathway_inference

changeset 4:6c30272fb587 draft

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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
files decoupler_pseudobulk.py
diffstat 1 files changed, 15 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- a/decoupler_pseudobulk.py	Mon Jul 15 10:56:37 2024 +0000
+++ b/decoupler_pseudobulk.py	Sun Sep 15 09:56:39 2024 +0000
@@ -320,6 +320,21 @@
         min_counts=args.min_counts,
     )
 
+    print("Created pseudo-bulk AnnData, checking if fields still make sense.")
+    print(
+        "If this fails this check, it might mean that you asked for factors "
+        + "that are not compatible with you sample identifiers (ie. asked for "
+        + "phase in the factors, but each sample contains more than one phase, "
+        + "try joining fields)"
+    )
+    if factor_fields:
+        check_fields(
+            factor_fields,
+            pseudobulk_data,
+            context=" after creation of pseudo-bulk AnnData",
+        )
+    print("Factors requested are adequate for the pseudo-bulked AnnData!")
+
     # Plot pseudobulk samples
     plot_pseudobulk_samples(
         pseudobulk_data,