Fixed an error in construct_landscape of ov.space.STT

Starlitnightly · Jul 25, 2024 · efa3e16 · efa3e16
1 parent 09e667b
commit efa3e16
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Showing 3 changed files with 28 additions and 2 deletions.
diff --git a/omicverse/bulk2single/_bulk2single.py b/omicverse/bulk2single/_bulk2single.py
@@ -35,8 +35,11 @@ def __init__(self,bulk_data:pd.DataFrame,single_data:anndata.AnnData,
             gpu: The ID of the GPU to use. Set to -1 to use CPU. Default is 0. If set to 'mps', the MPS backend will be used.
 
         """
+        single_data.var_names_make_unique()
+        bulk_data=data_drop_duplicates_index(bulk_data)
         self.bulk_data=bulk_data
         self.single_data=single_data
+
         if self.single_data.shape[0]>max_single_cells:
             print(f"......random select {max_single_cells} single cells")
             import random

diff --git a/omicverse/externel/STT/tl/_construct_landscape.py b/omicverse/externel/STT/tl/_construct_landscape.py
@@ -32,17 +32,32 @@ def construct_landscape(sc_object,thresh_cal_cov = 0.3, scale_axis = 1.0, scale_
     mu_hat = sc_object.uns['da_out']['mu_hat']
     rho = sc_object.obsm['rho']
     projection = sc_object.obsm[coord_key][:,0:2]
+    p_hat=adata.uns['da_out']['P_hat']
 
 
     labels = np.argmax(rho,axis = 1)
     K = max(labels)+1
+
+    while K<rho.shape[1]:
+        rho=rho[:,:-1]
+        mu_hat=mu_hat[:-1]
+        mu_hat = mu_hat / np.sum(mu_hat)
+        p_hat=p_hat[:-1,:-1]
+        p_hat=(p_hat.T/np.sum(p_hat, axis=1)).T
+
+    sc_object.obsm['rho']=rho
+    sc_object.uns['da_out']['mu_hat']=mu_hat
+    sc_object.uns['da_out']['P_hat']=p_hat
+
+
 
     centers = []
     for i in range(K):
         index = labels==i
         p = np.mean(projection[index], axis=0)
         centers.append(p)
     centers = np.array(centers)
+    centers = np.nan_to_num(centers, nan=0.0)
 
     trans_coord = np.matmul(rho,centers)
 

diff --git a/omicverse_guide/docs/Release_notes.md b/omicverse_guide/docs/Release_notes.md
@@ -423,5 +423,13 @@ Support Raw Windows platform
 
 ### Bulk Module
 
-- Fiexed an key error in `ov.bulk.Matrix_ID_mapping`
-- Added `enrichment_multi_concat` in `ov.bulk` to concat the result of enrichment.
+- Fixed an key error in `ov.bulk.Matrix_ID_mapping`
+- Added `enrichment_multi_concat` in `ov.bulk` to concat the result of enrichment.
+
+### Bulk Module
+
+- Added `adata.var_names_make_unique()` to avoid mat shape error if gene not unique. #100
+
+### Space Module
+
+- Fixed an error in `construct_landscape` of `ov.space.STT`