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YangLabHKUST · Jul 7, 2023 · 71b0141 · 71b0141
1 parent 2a39ac6
commit 71b0141
Showing 1 changed file with 4 additions and 1 deletion.
diff --git a/STitch3D/utils.py b/STitch3D/utils.py
@@ -18,6 +18,8 @@ def align_spots(adata_st_list_input, # list of spatial transcriptomics datasets
  tol=0.01, # parameter for "icp" method; tolerance level
  test_all_angles=False, # parameter for "icp" method; whether to test multiple rotation angles or not
  plot=False,
+ paste_alpha=0.1,
+ paste_dissimilarity="kl"
  ):
  # Align coordinates of spatial transcriptomics
 
@@ -116,7 +118,8 @@ def align_spots(adata_st_list_input, # list of spatial transcriptomics datasets
  pis = []
  # Calculate pairwise transformation matrices
  for i in range(len(adata_st_list) - 1):
- pi = pairwise_align_paste(adata_st_list[i], adata_st_list[i+1], coor_key=coor_key)
+ pi = pairwise_align_paste(adata_st_list[i], adata_st_list[i+1], coor_key=coor_key,
+ alpha = paste_alpha, dissimilarity = paste_dissimilarity)
  pis.append(pi)
  # Tranform
  S1, S2 = generalized_procrustes_analysis(adata_st_list[0].obsm[coor_key],