exprmat 0.1.33__tar.gz → 0.1.35__tar.gz

{exprmat-0.1.33 → exprmat-0.1.35}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: exprmat
-Version: 0.1.33
+Version: 0.1.35
 Classifier: Programming Language :: Rust
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy
@@ -63,6 +63,11 @@ Requires-Dist: scikit-image
 Requires-Dist: spatial-image
 Requires-Dist: multiscale-spatial-image
 Requires-Dist: tangram-sc
+Requires-Dist: shapely>=2.0.0
+Requires-Dist: pyogrio>=0.7.2
+Requires-Dist: pyproj>=3.3.0
+Requires-Dist: geopandas
+Requires-Dist: packaging
 Requires-Dist: sphinx ; extra == 'dev'
 Requires-Dist: twine ; extra == 'dev'
 Requires-Dist: ipykernel ; extra == 'dev'

{exprmat-0.1.33 → exprmat-0.1.35}/exprmat/__init__.py

@@ -10,12 +10,13 @@ import anndata as ad
 import scanpy as sc
 import pandas as pd
 import pathlib
+from PIL import Image
 
 from exprmat.configuration import default as config
 from exprmat.ansi import warning, info
 
 mu.set_options(pull_on_update = False)
-
+Image.MAX_IMAGE_PIXELS = config['max.image']
 
 DATABASE_SETUP_MESSAGE = """
 The exprmat package do not come with a included database after version 0.1.25, 

{exprmat-0.1.33 → exprmat-0.1.35}/exprmat/configuration.py

@@ -38,6 +38,8 @@ class Configuration:
             'hsa': 'grch38'
         }
 
+        self.config['max.image'] = int(10000 * 50000)
+
 
     def __getitem__(self, index):
         return self.config[index]

{exprmat-0.1.33 → exprmat-0.1.35}/exprmat/descriptive/gse.py

@@ -14,6 +14,7 @@ def gse(
     de_slot, group_name = None,
     min_pct = 0.0, max_pct_reference = 1, 
     min_lfc = None, max_lfc = None, remove_zero_pval = False,
+    max_q = 0.05,
 
     key_added = 'gsea',
     gene_sets = 'all',
@@ -46,6 +47,8 @@ def gse(
         tab = tab[tab['lfc'] >= min_lfc]
     if max_lfc is not None and 'lfc' in tab.columns:
         tab = tab[tab['lfc'] <= max_lfc]
+    if max_q is not None and 'q' in tab.columns:
+        tab = tab[tab['q'] <= max_q]
     if remove_zero_pval:
         tab = tab[~ np.isinf(tab['log10.q'].to_numpy())]
     
@@ -117,6 +120,7 @@ def opa(
     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,
+    max_q = 0.05,
 
     key_added = 'opa',
     gene_sets = 'kegg',
@@ -152,6 +156,8 @@ 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 max_q is not None and 'q' in tab.columns:
+            tab = tab[tab['q'] <= max_q]
         
         if not use_abs_lfc:
             if min_lfc is not None and 'lfc' in tab.columns: