Fixed an error in ov.utils.roe when some expected frequencies are l…

…ess than expected value.
Starlitnightly · Jul 25, 2024 · b520a0d · b520a0d
1 parent efa3e16
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Showing 4 changed files with 20 additions and 7 deletions.
diff --git a/README.md b/README.md
@@ -177,7 +177,7 @@ If you use `omicverse` in your work, please cite the `omicverse` publication as
 >
 > Zeng, Z., Ma, Y., Hu, L. et al.
 >
-> _Nature Communication_ 2024 Jul 17. doi: [10.1038/s41467-024-50194-3](https://doi.org/10.1038/s41467-024-50194-3).
+> _Nature Communication_ 2024 Jul 16. doi: [10.1038/s41467-024-50194-3](https://doi.org/10.1038/s41467-024-50194-3).
 
 
 ## `8` [Other](#)

diff --git a/omicverse/externel/spatrio/spatrio.py b/omicverse/externel/spatrio/spatrio.py
@@ -26,7 +26,7 @@ def ot_alignment(
     norm: str = 'l2', 
     backend = None,  
     return_obj: bool = False,
-    verbose: bool = False, 
+    verbose: bool = True, 
     k: int = 10,
     graph_mode: str = "connectivity",
     aware_spatial: bool = True,
@@ -541,14 +541,20 @@ def f(G):
     def df(G):
         return ot.gromov.gwggrad(constC, hC1, hC2, G)
     if log:
-        res, log = ot.gromov.cg(p, q, (1 - alpha) * M, alpha, f, df, G0, armijo=armijo, C1=C1, C2=C2, constC=constC, log=True, numItermaxEmd=numItermaxEmd, **kwargs)
-
+        if ot.__version__ < '0.9.0':
+            res, log = ot.gromov.cg(p, q, (1 - alpha) * M, alpha, f, df, G0, armijo=armijo, C1=C1, C2=C2, constC=constC, log=True, numItermaxEmd=numItermaxEmd, **kwargs)
+        else:
+            res, log = ot.optim.cg(p, q, (1 - alpha) * M, alpha, f, df, G0, armijo=armijo, C1=C1, C2=C2, constC=constC, log=True, numItermaxEmd=numItermaxEmd, **kwargs)
+
         fgw_dist = log['loss'][-1]
 
         log['fgw_dist'] = fgw_dist
         log['u'] = log['u']
         log['v'] = log['v']
         return res, log
     else:
-        return ot.gromov.cg(p, q, (1 - alpha) * M, alpha, f, df, G0, armijo=armijo, C1=C1, C2=C2, constC=constC, **kwargs)
-
+        if ot.__version__ < '0.9.0':
+            return ot.gromov.cg(p, q, (1 - alpha) * M, alpha, f, df, G0, armijo=armijo, C1=C1, C2=C2, constC=constC, **kwargs)
+        else:
+            return ot.optim.cg(p, q, (1 - alpha) * M, alpha, f, df, G0, armijo=armijo, C1=C1, C2=C2, constC=constC, **kwargs)
+
diff --git a/omicverse/utils/_roe.py b/omicverse/utils/_roe.py
@@ -55,6 +55,9 @@ def roe(
                 f"Some expected frequencies are less than {expected_value_threshold}, it is suggested to use other statistical methods, such as Fisher's exact test")
             expected_data = pd.DataFrame(expected, index=num_cell.index, columns=num_cell.columns)
             adata.uns['expected_values'] = expected_data
+            roe = num_cell / expected_data
+            adata.uns['roe_results'] = roe
+            adata.uns['unsig_roe_results'] = roe
     else:
         print("P-value is greater than 0.05, there is no statistical significance")
         roe_ratio = num_cell / expected

diff --git a/omicverse_guide/docs/Release_notes.md b/omicverse_guide/docs/Release_notes.md
@@ -420,13 +420,17 @@ Support Raw Windows platform
 ### Pl Module
 
 - Fixed the 'celltyep_key' error of `ov.pl.cpdb_group_heatmap` #109
+- Fixed an error in `ov.utils.roe` when some expected frequencies are less than expected value.
+
+### Single Module
+- Fixed the bug of `ov.single.cytotrace2` when adata.X is not sparse data. #115, #116
 
 ### Bulk Module
 
 - 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
+### Bulk2Single Module
 
 - Added `adata.var_names_make_unique()` to avoid mat shape error if gene not unique. #100