Merge 4af9d8f into c804ea5

angelolab · Nov 9, 2020 · 5905440 · 5905440
2 parents c804ea5 + 4af9d8f
commit 5905440
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Showing 3 changed files with 8 additions and 16 deletions.
diff --git a/ark/analysis/spatial_analysis.py b/ark/analysis/spatial_analysis.py
@@ -299,6 +299,10 @@ def create_neighborhood_matrix(all_data, dist_matrices_dict, included_fovs=None,
         cell_neighbor_counts.loc[current_fov_neighborhood_data.index, fov_cluster_names] = counts
         cell_neighbor_freqs.loc[current_fov_neighborhood_data.index, fov_cluster_names] = freqs
 
+    # drop label column, as this interferes with the neighborhood clustering step
+    cell_neighbor_counts = cell_neighbor_counts.drop(columns=cell_label_col)
+    cell_neighbor_freqs = cell_neighbor_freqs.drop(columns=cell_label_col)
+
     return cell_neighbor_counts, cell_neighbor_freqs
 
 

diff --git a/ark/analysis/spatial_analysis_test.py b/ark/analysis/spatial_analysis_test.py
@@ -238,8 +238,6 @@ def test_generate_cluster_matrix_results():
         all_data_pos, dist_mat_pos, distlim=51
     )
 
-    neighbor_counts = neighbor_counts.drop(settings.CELL_LABEL, axis=1)
-
     # error checking
     with pytest.raises(ValueError):
         # pass bad columns