Merge pull request #31 from earmingol/new_version

cell2cell v0.6.8

cell2cell/__init__.py

@@ -12,4 +12,4 @@
 from cell2cell import tensor
 from cell2cell import utils
 
-__version__ = "0.6.7"
+__version__ = "0.6.8"

cell2cell/external/gseapy.py

@@ -233,7 +233,7 @@ def run_gsea(loadings, lr_set, output_folder, weight=1, min_size=15, permutation
     terms = []
     factors = []
     nes = []
-    for factor in loadings.columns[1:]:
+    for factor in df.columns[1:]:
         p_report = pd.read_csv(output_folder + '/GSEA/' + factor + '/gseapy.gene_set.prerank.report.csv')
         pval = p_report['NOM p-val'].values.tolist()
         pvals.extend(pval)
@@ -254,7 +254,7 @@ def run_gsea(loadings, lr_set, output_folder, weight=1, min_size=15, permutation
     scores = gsea_df.pivot(index="Term", columns="Factor", values="NES").fillna(0)
 
     # Sort factors
-    sorted_columns = [f for f in loadings.columns[1:] if (f in pvals.columns) & (f in scores.columns)]
+    sorted_columns = [f for f in df.columns[1:] if (f in pvals.columns) & (f in scores.columns)]
     pvals = pvals[sorted_columns]
     scores = scores[sorted_columns]
     return pvals, scores, gsea_df

release/0.6.8-notes.md

@@ -0,0 +1,10 @@
+# Release Notes - cell2cell v0.6.8
+
+## New features
+
+
+## Feature updates
+
+
+## Fixed Bugs
+- Fixed bug that was skipping first factor to generate outputs from `cell2cell.external.gseapy.run_gsea()`