version 1.1.2

Author: mrland99

build/lib/paste/PASTE.py

@@ -61,13 +61,13 @@ def pairwise_align(sliceA, sliceB, alpha = 0.1, G_init = None, a_distribution =
         return pi, logw['fgw_dist']
     return pi
 
-def center_align(A, slices, lmbda, alpha = 0.1, n_components = 15, threshold = 0.001, max_iter = 10, norm = False, random_seed = None, pis_init = None, verbose = False):
+def center_align(A, slices, lmbda = None, alpha = 0.1, n_components = 15, threshold = 0.001, max_iter = 10, norm = False, random_seed = None, pis_init = None, verbose = False):
     """
     Computes center alignment of slices.
     
     param: A - Initialization of starting AnnData Spatial Object; Make sure to include gene expression AND spatial info
     param: slices - List of slices (AnnData objects) used to calculate center alignment
-    param: lmbda - List of probability weights assigned to each slice
+    param: lmbda - List of probability weights assigned to each slice; default is uniform weights
     param: n_components - Number of components in NMF decomposition
     param: threshold - Threshold for convergence of W and H
     param: max_iter - maximum number of iterations for solving for center slice
@@ -81,6 +81,9 @@ def center_align(A, slices, lmbda, alpha = 0.1, n_components = 15, threshold = 0
     return: pi - List of pairwise alignment mappings of the center slice (rows) to each input slice (columns)
     """
 
+    if lmbda is None:
+        lmbda = len(slices)*[1/len(slices)]
+    
     # get common genes
     common_genes = A.var.index
     for s in slices:
@@ -104,9 +107,13 @@ def center_align(A, slices, lmbda, alpha = 0.1, n_components = 15, threshold = 0
     H = model.components_
     center_coordinates = A.obsm['spatial']
 
+    if not isinstance(center_coordinates, np.ndarray):
+        print("Warning: A.obsm['spatial'] is not of type numpy array .")
+    
     # Initialize center_slice
     center_slice = anndata.AnnData(np.dot(W,H))
     center_slice.var.index = common_genes
+    center_slice.obs.index = A.obs.index
     center_slice.obsm['spatial'] = center_coordinates
 
     # Minimize R

dist/paste-bio-1.1.0.tar.gz

@@ -1,6 +1,6 @@
 [metadata]
 name = paste-bio
-version = 1.1.1
+version = 1.1.2
 author = Max Land
 author_email = max.ruikang.land@gmail.com
 description = A computational method to align and integrate spatial transcriptomics experiments.

dist/paste-bio-1.1.1.tar.gz

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: paste-bio
-Version: 1.1.1
+Version: 1.1.2
 Summary: A computational method to align and integrate spatial transcriptomics experiments.
 Home-page: https://github.com/raphael-group/paste
 Author: Max Land