spacr 0.3.66__py3-none-any.whl → 0.3.70__py3-none-any.whl

spacr/io.py

@@ -2456,7 +2456,8 @@ def _read_and_merge_data(locs, tables, verbose=False, nuclei_limit=10, pathogen_
     for idx, loc in enumerate(locs):
         db_dfs = _read_db(loc, tables)
         if change_plate:
-            db_dfs['plate'] = f'plate{idx}'
+            db_dfs['plate'] = f'plate{idx+1}'
+            db_dfs['prc'] = db_dfs['plate'].astype(str) + '_' + db_dfs['row_name'].astype(str) + '_' + db_dfs['column_name'].astype(str)
         for table, df in zip(tables, db_dfs):
             data_dict[table].append(df)
 

spacr/ml.py

@@ -1493,27 +1493,32 @@ def _calculate_similarity(df, features, col_to_compare, val1, val2):
         # Add a small value to the diagonal elements for regularization
         epsilon = 1e-5
         inv_cov_matrix = np.linalg.inv(cov_matrix + np.eye(cov_matrix.shape[0]) * epsilon)
-    
+        
     # Calculate similarity scores
-    df['similarity_to_pos_euclidean'] = df[features].apply(lambda row: euclidean(row, pos_control), axis=1)
-    df['similarity_to_neg_euclidean'] = df[features].apply(lambda row: euclidean(row, neg_control), axis=1)
-    df['similarity_to_pos_cosine'] = df[features].apply(lambda row: cosine(row, pos_control), axis=1)
-    df['similarity_to_neg_cosine'] = df[features].apply(lambda row: cosine(row, neg_control), axis=1)
-    df['similarity_to_pos_mahalanobis'] = df[features].apply(lambda row: mahalanobis(row, pos_control, inv_cov_matrix), axis=1)
-    df['similarity_to_neg_mahalanobis'] = df[features].apply(lambda row: mahalanobis(row, neg_control, inv_cov_matrix), axis=1)
-    df['similarity_to_pos_manhattan'] = df[features].apply(lambda row: cityblock(row, pos_control), axis=1)
-    df['similarity_to_neg_manhattan'] = df[features].apply(lambda row: cityblock(row, neg_control), axis=1)
-    df['similarity_to_pos_minkowski'] = df[features].apply(lambda row: minkowski(row, pos_control, p=3), axis=1)
-    df['similarity_to_neg_minkowski'] = df[features].apply(lambda row: minkowski(row, neg_control, p=3), axis=1)
-    df['similarity_to_pos_chebyshev'] = df[features].apply(lambda row: chebyshev(row, pos_control), axis=1)
-    df['similarity_to_neg_chebyshev'] = df[features].apply(lambda row: chebyshev(row, neg_control), axis=1)
-    df['similarity_to_pos_hamming'] = df[features].apply(lambda row: hamming(row, pos_control), axis=1)
-    df['similarity_to_neg_hamming'] = df[features].apply(lambda row: hamming(row, neg_control), axis=1)
-    df['similarity_to_pos_jaccard'] = df[features].apply(lambda row: jaccard(row, pos_control), axis=1)
-    df['similarity_to_neg_jaccard'] = df[features].apply(lambda row: jaccard(row, neg_control), axis=1)
-    df['similarity_to_pos_braycurtis'] = df[features].apply(lambda row: braycurtis(row, pos_control), axis=1)
-    df['similarity_to_neg_braycurtis'] = df[features].apply(lambda row: braycurtis(row, neg_control), axis=1)
-    
+    def safe_similarity(func, row, control):
+        try:
+            return func(row, control)
+        except Exception:
+            return np.nan
+        
+    # Calculate similarity scores
+    try:
+        df['similarity_to_pos_euclidean'] = df[features].apply(lambda row: safe_similarity(euclidean, row, pos_control), axis=1)
+        df['similarity_to_neg_euclidean'] = df[features].apply(lambda row: safe_similarity(euclidean, row, neg_control), axis=1)
+        df['similarity_to_pos_cosine'] = df[features].apply(lambda row: safe_similarity(cosine, row, pos_control), axis=1)
+        df['similarity_to_neg_cosine'] = df[features].apply(lambda row: safe_similarity(cosine, row, neg_control), axis=1)
+        df['similarity_to_pos_mahalanobis'] = df[features].apply(lambda row: safe_similarity(mahalanobis, row, pos_control, inv_cov_matrix), axis=1)
+        df['similarity_to_neg_mahalanobis'] = df[features].apply(lambda row: safe_similarity(mahalanobis, row, neg_control, inv_cov_matrix), axis=1)
+        df['similarity_to_pos_manhattan'] = df[features].apply(lambda row: safe_similarity(cityblock, row, pos_control), axis=1)
+        df['similarity_to_neg_manhattan'] = df[features].apply(lambda row: safe_similarity(cityblock, row, neg_control), axis=1)
+        df['similarity_to_pos_minkowski'] = df[features].apply(lambda row: safe_similarity(minkowski, row, pos_control, p=3), axis=1)
+        df['similarity_to_neg_minkowski'] = df[features].apply(lambda row: safe_similarity(minkowski, row, neg_control, p=3), axis=1)
+        df['similarity_to_pos_chebyshev'] = df[features].apply(lambda row: safe_similarity(chebyshev, row, pos_control), axis=1)
+        df['similarity_to_neg_chebyshev'] = df[features].apply(lambda row: safe_similarity(chebyshev, row, neg_control), axis=1)
+        df['similarity_to_pos_braycurtis'] = df[features].apply(lambda row: safe_similarity(braycurtis, row, pos_control), axis=1)
+        df['similarity_to_neg_braycurtis'] = df[features].apply(lambda row: safe_similarity(braycurtis, row, neg_control), axis=1)
+    except Exception as e:
+        print(f"Error calculating similarity scores: {e}")    
     return df
 
 def interperate_vision_model(settings={}):

spacr/plot.py

@@ -3771,7 +3771,7 @@ def plot_proportion_stacked_bars(settings, df, group_column, bin_column, prc_col
     pairwise_results = chi_pairwise(raw_counts, verbose=settings.get('verbose', False))
 
     # Plot based on level setting
-    if level == 'well':
+    if level in ['well', 'plate']:
         # Aggregate by well for mean ± SD visualization
         well_proportions = (
             df.groupby([group_column, prc_column, bin_column])

{spacr-0.3.66.dist-info → spacr-0.3.70.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.3.66
+Version: 0.3.70
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson

{spacr-0.3.66.dist-info → spacr-0.3.70.dist-info}/RECORD

@@ -15,13 +15,13 @@ spacr/gui.py,sha256=ARyn9Q_g8HoP-cXh1nzMLVFCKqthY4v2u9yORyaQqQE,8230
 spacr/gui_core.py,sha256=N7R7yvfK_dJhOReM_kW3Ci8Bokhi1OzsxeKqvSGdvV4,41460
 spacr/gui_elements.py,sha256=EKlvEg_4_je7jciEdR3NTgPrcTraowa2e2RUt-xqd6M,138254
 spacr/gui_utils.py,sha256=u9RoIOWpAXFEOnUlLpMQZrc1pWSg6omZsJMIhJdRv_g,41211
-spacr/io.py,sha256=SLJKVqe5c3dFa6a7tXA5KMGhNGjhvLbyqsPlD1AqM3g,142962
+spacr/io.py,sha256=ActzerMS0NC1-MIffGTFBdKcqL1T72d3VjfieTta3O4,143101
 spacr/logger.py,sha256=lJhTqt-_wfAunCPl93xE65Wr9Y1oIHJWaZMjunHUeIw,1538
 spacr/measure.py,sha256=2lK-ZcTxLM-MpXV1oZnucRD9iz5aprwahRKw9IEqshg,55085
 spacr/mediar.py,sha256=FwLvbLQW5LQzPgvJZG8Lw7GniA2vbZx6Jv6vIKu7I5c,14743
-spacr/ml.py,sha256=GOQJH8jdTrJQwiLlDrcc9-yCxLFaMx4YD4OJs0-R5YI,77947
+spacr/ml.py,sha256=h0IrXoNnyNzZLPYbtZPFI6c4Qeu1gH8R3iUz_O7-ar0,78114
 spacr/openai.py,sha256=5vBZ3Jl2llYcW3oaTEXgdyCB2aJujMUIO5K038z7w_A,1246
-spacr/plot.py,sha256=XPAabtZjzurL6zlG3KfqLEQTnH_jjo-k2jVajJt9om8,165166
+spacr/plot.py,sha256=gXC7y3uT4sx8KRODeSFWQG_A1CylsuJ5B7HYe_un6so,165177
 spacr/sequencing.py,sha256=ClUfwPPK6rNUbUuiEkzcwakzVyDKKUMv9ricrxT8qQY,25227
 spacr/settings.py,sha256=wZcqdTWaRus27wn9P0EGyftcJn_i0IwlM9pyeCVqxr8,80173
 spacr/sim.py,sha256=1xKhXimNU3ukzIw-3l9cF3Znc_brW8h20yv8fSTzvss,71173
@@ -152,9 +152,9 @@ spacr/resources/icons/umap.png,sha256=dOLF3DeLYy9k0nkUybiZMe1wzHQwLJFRmgccppw-8b
 spacr/resources/images/plate1_E01_T0001F001L01A01Z01C02.tif,sha256=Tl0ZUfZ_AYAbu0up_nO0tPRtF1BxXhWQ3T3pURBCCRo,7958528
 spacr/resources/images/plate1_E01_T0001F001L01A02Z01C01.tif,sha256=m8N-V71rA1TT4dFlENNg8s0Q0YEXXs8slIn7yObmZJQ,7958528
 spacr/resources/images/plate1_E01_T0001F001L01A03Z01C03.tif,sha256=Pbhk7xn-KUP6RSIhJsxQcrHFImBm3GEpLkzx7WOc-5M,7958528
-spacr-0.3.66.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
-spacr-0.3.66.dist-info/METADATA,sha256=A5XJI5cR864WLb08NonbMW2BEUHYn-fQgl8RMcdIK8M,6032
-spacr-0.3.66.dist-info/WHEEL,sha256=HiCZjzuy6Dw0hdX5R3LCFPDmFS4BWl8H-8W39XfmgX4,91
-spacr-0.3.66.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
-spacr-0.3.66.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
-spacr-0.3.66.dist-info/RECORD,,
+spacr-0.3.70.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
+spacr-0.3.70.dist-info/METADATA,sha256=152VlHisIA_E2F9NYFd_pqDqVxqpGZ07qUDzb7BTnPc,6032
+spacr-0.3.70.dist-info/WHEEL,sha256=HiCZjzuy6Dw0hdX5R3LCFPDmFS4BWl8H-8W39XfmgX4,91
+spacr-0.3.70.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
+spacr-0.3.70.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
+spacr-0.3.70.dist-info/RECORD,,