fixed geneset scoring

Author: pcahan1

docs/CHANGELOG.md

@@ -4,6 +4,10 @@ All notable changes to PySingleCellNet should be listed here. The definition of
 
 ## [Unreleased]
 
+# TO FIX
+
+tl.score_gene_sets should add scores, one matrix to .obsm and not as columsn to .obs
+
 ### Changed
 - tl.cluster_subclusters layer should be None instead of counts 
 

src/pySingleCellNet/__init__.py

@@ -1,17 +1,19 @@
 """PySingleCellNet"""
 
 from .config import SCN_CATEGORY_COLOR_DICT 
-from .config import SCN_DIFFEXP_KEY
-from . import plotting as pl
-from . import utils as ut
-from . import tools as tl
+from .config import SCN_DIFFEXP_KEY
+from . import plotting as pl
+from . import utils as ut
+from . import tools as tl
+from . import string_io as st
 
 # Public API
-__all__ = [
-    "__version__",
-    "pl",
-    "ut",
-    "tl"
-]    
+__all__ = [
+    "__version__",
+    "pl",
+    "ut",
+    "tl",
+    "st",
+]    
 
 

src/pySingleCellNet/tools/__init__.py

@@ -37,7 +37,9 @@
     name_gene_modules_by_annotation,
     whoare_genes_neighbors,
     what_module_has_gene,
-    find_string_physical_modules,
+    find_string_network_modules,
+    find_hybrid_gene_modules,
+    load_string_links_df,
     score_gene_sets,
     correlate_module_scores_with_pcs
 )
@@ -64,7 +66,9 @@
     "name_gene_modules_by_annotation",
     "whoare_genes_neighbors",
     "what_module_has_gene",
-    "find_string_physical_modules",
+    "find_string_network_modules",
+    "find_hybrid_gene_modules",
+    "load_string_links_df",
     "score_gene_sets",
     "correlate_module_scores_with_pcs"
 ]