Fixes #892

MaayanLab · Oct 16, 2023 · ec407ab · ec407ab
1 parent 3c63efc
commit ec407ab
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/appyters/Bulk_RNA_seq/appyter.json b/appyters/Bulk_RNA_seq/appyter.json
@@ -2,7 +2,7 @@
   "$schema": "https://raw.githubusercontent.com/MaayanLab/appyter-catalog/main/schema/appyter-validator.json",
   "name": "Bulk_RNA_seq",
   "title": "Bulk RNA-seq analysis pipeline",
-  "version": "0.1.7",
+  "version": "0.1.8",
   "description": "Bulk RNA-seq analysis pipeline enables you to analyze and visualize datasets with state-of-the-art algorithms and visualization methods.",
   "image": "screenshot.png",
   "authors": [

diff --git a/appyters/Bulk_RNA_seq/utils.py b/appyters/Bulk_RNA_seq/utils.py
@@ -424,15 +424,15 @@ def get_signatures(classes, dataset, normalization, method, meta_class_column_na
         elif method == "edgeR":
             edgeR = robjects.r['edgeR']
 
-            edgeR_results = pandas2ri.conversion.rpy2py(edgeR(pandas2ri.conversion.py2rpy(expr_df), pandas2ri.conversion.py2rpy(cls1_sample_ids), pandas2ri.conversion.py2rpy(cls2_sample_ids)))
+            edgeR_results = pandas2ri.conversion.rpy2py(edgeR(pandas2ri.conversion.py2rpy(expr_df.loc[:, cls1_sample_ids+cls2_sample_ids]), pandas2ri.conversion.py2rpy(cls1_sample_ids), pandas2ri.conversion.py2rpy(cls2_sample_ids)))
 
             signature = pd.DataFrame(edgeR_results[0])
             signature.index = edgeR_results[1]
             signature = signature.sort_values("logFC", ascending=False)
         elif method == "DESeq2":
             # deseq2 receives raw counts
             DESeq2 = robjects.r['deseq2']
-            DESeq2_results = pandas2ri.conversion.rpy2py(DESeq2(pandas2ri.conversion.py2rpy(expr_df), pandas2ri.conversion.py2rpy(cls1_sample_ids), pandas2ri.conversion.py2rpy(cls2_sample_ids)))
+            DESeq2_results = pandas2ri.conversion.rpy2py(DESeq2(pandas2ri.conversion.py2rpy(expr_df.loc[:, cls1_sample_ids+cls2_sample_ids]), pandas2ri.conversion.py2rpy(cls1_sample_ids), pandas2ri.conversion.py2rpy(cls2_sample_ids)))
 
             signature = pd.DataFrame(DESeq2_results[0])
             signature.index = DESeq2_results[1]