Fix subset operation on SingleCellExperiment slots (#29)

BiocPy · Jan 14, 2024 · d759ba6 · d759ba6
1 parent 73491d2
commit d759ba6
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Showing 2 changed files with 6 additions and 12 deletions.
diff --git a/src/singlecellexperiment/SingleCellExperiment.py b/src/singlecellexperiment/SingleCellExperiment.py
@@ -921,18 +921,15 @@ def get_slice(
 
         new_reduced_dims = {}
         for rdim, rmat in self._reduced_dims.items():
-            if slicer.row_indices != slice(None):
-                rmat = rmat[slicer.row_indices, :]
-
             if slicer.col_indices != slice(None):
-                rmat = rmat[:, slicer.col_indices]
+                rmat = rmat[slicer.col_indices, :]
 
             new_reduced_dims[rdim] = rmat
 
         new_alt_expts = {}
         for altname, altexpt in self._alternative_experiments.items():
             if slicer.row_indices != slice(None):
-                altexpt = altexpt[rows, :]
+                altexpt = altexpt[slicer.row_indices, :]
 
             if slicer.col_indices != slice(None):
                 altexpt = altexpt[:, slicer.col_indices]
@@ -944,16 +941,10 @@ def get_slice(
             if slicer.row_indices != slice(None):
                 rpair = rpair[slicer.row_indices, :]
 
-            if slicer.col_indices != slice(None):
-                rpair = rpair[:, slicer.col_indices]
-
             new_row_pairs[rname] = rpair
 
         new_col_pairs = {}
         for cname, cpair in self._column_pairs.items():
-            if slicer.row_indices != slice(None):
-                cpair = cpair[slicer.row_indices, :]
-
             if slicer.col_indices != slice(None):
                 cpair = cpair[:, slicer.col_indices]
 

diff --git a/tests/test_sce_slice.py b/tests/test_sce_slice.py
@@ -51,7 +51,10 @@
 
 def test_SCE_slice():
     tse = SingleCellExperiment(
-        assays={"counts": counts}, row_data=row_data, column_data=col_data
+        assays={"counts": counts},
+        row_data=row_data,
+        column_data=col_data,
+        reduced_dims={"random_embeds": np.random.rand(ncols, 5)},
     )
 
     tse_slice = tse[0:10, 0:3]