exprmat 0.1.17__tar.gz → 0.1.18__tar.gz

{exprmat-0.1.17 → exprmat-0.1.18}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: exprmat
-Version: 0.1.17
+Version: 0.1.18
 Summary: routines to process expression matrices
 Home-page: https://github.com/yang-z-03/exprmat
 Author: Zheng Yang

{exprmat-0.1.17 → exprmat-0.1.18}/exprmat/__init__.py

@@ -4,4 +4,4 @@ import anndata as ad
 
 mu.set_options(pull_on_update = False)
 
-def version(): return 'exprmat 0.1.17-1 [dev]'
+def version(): return 'exprmat 0.1.18-1 [dev]'

{exprmat-0.1.17 → exprmat-0.1.18}/exprmat/descriptive/gse.py

@@ -107,10 +107,11 @@ def opa(
     de_slot, group_name = None, translate_de_slot = None,
     min_pct = 0.0, max_pct_reference = 1, 
     min_lfc = None, max_lfc = None, remove_zero_pval = False,
+    use_abs_lfc = False, min_abs_lfc = 1.0, max_abs_lfc = 25.0,
 
     key_added = 'opa',
     gene_sets = 'kegg',
-    identifier = 'uppercase',
+    identifier = 'entrez',
     opa_cutoff = 0.05,
 ):
     
@@ -133,10 +134,16 @@ def opa(
             tab = tab[tab['pct'] >= min_pct]
         if max_pct_reference is not None and 'pct.reference' in tab.columns:
             tab = tab[tab['pct.reference'] <= max_pct_reference]
-        if min_lfc is not None and 'lfc' in tab.columns:
-            tab = tab[tab['lfc'] >= min_lfc]
-        if max_lfc is not None and 'lfc' in tab.columns:
-            tab = tab[tab['lfc'] <= max_lfc]
+        
+        if not use_abs_lfc:
+            if min_lfc is not None and 'lfc' in tab.columns:
+                tab = tab[tab['lfc'] >= min_lfc]
+            if max_lfc is not None and 'lfc' in tab.columns:
+                tab = tab[tab['lfc'] <= max_lfc]
+        else:
+            tab = tab[np.abs(tab['lfc'].to_numpy()) >= min_abs_lfc]
+            tab = tab[np.abs(tab['lfc'].to_numpy()) <= max_abs_lfc]
+
         if remove_zero_pval:
             tab = tab[~ np.isinf(tab['log10.q'].to_numpy())]
         

{exprmat-0.1.17 → exprmat-0.1.18}/exprmat/reader/experiment.py

@@ -1157,6 +1157,7 @@ class experiment:
         de_slot, group_name = None,
         min_pct = 0.0, max_pct_reference = 1, 
         min_lfc = None, max_lfc = None, remove_zero_pval = False,
+        use_abs_lfc = False, min_abs_lfc = 1.0, max_abs_lfc = 25.0,
 
         key_added = 'gsea',
         gene_sets = 'all',
@@ -1169,6 +1170,7 @@ class experiment:
             adata, taxa = taxa, de_slot = de_slot, group_name = None,
             min_pct = min_pct, max_pct_reference = max_pct_reference,
             min_lfc = min_lfc, max_lfc = max_lfc, remove_zero_pval = remove_zero_pval,
+            use_abs_lfc = use_abs_lfc, min_abs_lfc = min_abs_lfc, max_abs_lfc = max_abs_lfc,
             key_added = key_added, gene_sets = gene_sets, identifier = identifier,
             opa_cutoff = opa_cutoff, **kwargs
         )

{exprmat-0.1.17 → exprmat-0.1.18}/exprmat.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: exprmat
-Version: 0.1.17
+Version: 0.1.18
 Summary: routines to process expression matrices
 Home-page: https://github.com/yang-z-03/exprmat
 Author: Zheng Yang

{exprmat-0.1.17 → exprmat-0.1.18}/setup.py

@@ -3,7 +3,7 @@ from setuptools import setup, find_packages
 
 setup(
     name                 = 'exprmat',
-    version              = '0.1.17',
+    version              = '0.1.18',
     description          = 'routines to process expression matrices',
     url                  = 'https://github.com/yang-z-03/exprmat',
     author               = 'Zheng Yang',