upgrade to v1.2.2

build/lib/paste/__init__.py

@@ -1,3 +1,3 @@
 from .PASTE import pairwise_align, center_align
-from .helper import match_spots_using_spatial_heuristic
+from .helper import match_spots_using_spatial_heuristic, filter_for_common_genes
 from .visualization import plot_slice, stack_slices_pairwise, stack_slices_center

build/lib/paste/helper.py

@@ -1,7 +1,26 @@
+from typing import List
+from anndata import AnnData
 import numpy as np
 import scipy
 import ot
 
+def filter_for_common_genes(
+    slices: List[AnnData]) -> None:
+    """
+    Filters for the intersection of genes between all slices.
+    
+    Args:
+        slices: List of slices.
+    """
+    assert len(slices) > 0, "Cannot have empty list."
+
+    common_genes = slices[0].var.index
+    for s in slices:
+        common_genes = intersect(common_genes, s.var.index)
+    for i in range(len(slices)):
+        slices[i] = slices[i][:, common_genes]
+    print('Filtered all slices for common genes. There are ' + str(len(common_genes)) + ' common genes.')
+
 def match_spots_using_spatial_heuristic(
     X,
     Y,

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = paste-bio
-version = 1.2.1
+version = 1.2.2
 author = Max Land
 author_email = max.ruikang.land@gmail.com
 description = A computational method to align and integrate spatial transcriptomics experiments.

src/paste_bio.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: paste-bio
-Version: 1.2.1
+Version: 1.2.2
 Summary: A computational method to align and integrate spatial transcriptomics experiments.
 Home-page: https://github.com/raphael-group/paste
 Author: Max Land