spacr 0.3.65__tar.gz → 0.3.66__tar.gz

{spacr-0.3.65/spacr.egg-info → spacr-0.3.66}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.3.65
+Version: 0.3.66
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson

{spacr-0.3.65 → spacr-0.3.66}/setup.py

@@ -69,7 +69,7 @@ dependencies = [
 
 setup(
     name="spacr",
-    version="0.3.65",
+    version="0.3.66",
     author="Einar Birnir Olafsson",
     author_email="olafsson@med.umich.com",
     description="Spatial phenotype analysis of crisp screens (SpaCr)",

{spacr-0.3.65 → spacr-0.3.66}/spacr/io.py

@@ -2445,7 +2445,7 @@ def _read_and_merge_data_v1(locs, tables, verbose=False, nuclei_limit=False, pat
         
     return merged_df, obj_df_ls 
 
-def _read_and_merge_data(locs, tables, verbose=False, nuclei_limit=10, pathogen_limit=10):
+def _read_and_merge_data(locs, tables, verbose=False, nuclei_limit=10, pathogen_limit=10, change_plate=False):
     from .io import _read_db
     from .utils import _split_data
 
@@ -2453,8 +2453,10 @@ def _read_and_merge_data(locs, tables, verbose=False, nuclei_limit=10, pathogen_
     data_dict = {table: [] for table in tables}
 
     # Extract plate DataFrames
-    for loc in locs:
+    for idx, loc in enumerate(locs):
         db_dfs = _read_db(loc, tables)
+        if change_plate:
+            db_dfs['plate'] = f'plate{idx}'
         for table, df in zip(tables, db_dfs):
             data_dict[table].append(df)
 

{spacr-0.3.65 → spacr-0.3.66}/spacr/plot.py

@@ -3737,7 +3737,7 @@ def graph_importance(settings):
     fig = spacr_graph.get_figure()
     plt.show()
     
-def plot_proportion_stacked_bars(settings, df, group_column, bin_column, prc_column='prc', level='object'):
+def plot_proportion_stacked_bars(settings, df, group_column, bin_column, prc_column='prc', level='object', cmap='viridis'):
     """
     Generate a stacked bar plot for proportions and perform chi-squared and pairwise tests.
     
@@ -3784,7 +3784,7 @@ def plot_proportion_stacked_bars(settings, df, group_column, bin_column, prc_col
         std_proportions = well_proportions.groupby(group_column).std()
 
         ax = mean_proportions.plot(
-            kind='bar', stacked=True, yerr=std_proportions, capsize=5, colormap='viridis', figsize=(12, 8)
+            kind='bar', stacked=True, yerr=std_proportions, capsize=5, colormap=cmap, figsize=(12, 8)
         )
         plt.title('Proportion of Volume Bins by Group (Mean ± SD across wells)')
     else:
@@ -3794,7 +3794,7 @@ def plot_proportion_stacked_bars(settings, df, group_column, bin_column, prc_col
         proportions = group_counts / group_totals
         proportion_df = proportions.unstack(fill_value=0)
 
-        ax = proportion_df.plot(kind='bar', stacked=True, colormap='viridis', figsize=(12, 8))
+        ax = proportion_df.plot(kind='bar', stacked=True, colormap=cmap, figsize=(12, 8))
         plt.title('Proportion of Volume Bins by Group')
 
     plt.xlabel('Group')

{spacr-0.3.65 → spacr-0.3.66}/spacr/settings.py

@@ -1415,6 +1415,8 @@ def set_analyze_endodyogeny_defaults(settings):
     settings.setdefault('um_per_px',0.1)
     settings.setdefault('max_bins',None)
     settings.setdefault('save',False)
+    settings.setdefault('change_plate',False)
+    settings.setdefault('cmap','viridis')
     settings.setdefault('verbose',False)
     return settings
 

{spacr-0.3.65 → spacr-0.3.66}/spacr/submodules.py

@@ -952,13 +952,17 @@ def analyze_endodyogeny(settings):
     for s in settings['src']:
         loc = os.path.join(s, 'measurements/measurements.db')
         locs.append(loc)
+        
+    if 'png_list' not in settings['tables']:
+        settings['tables'] = settings['tables'] + ['png_list']
     
     df, _ = _read_and_merge_data(
         locs, 
         tables=settings['tables'], 
         verbose=settings['verbose'], 
         nuclei_limit=settings['nuclei_limit'], 
-        pathogen_limit=settings['pathogen_limit']
+        pathogen_limit=settings['pathogen_limit'],
+        change_plate=settings['change_plate']
     )
     
     if not settings['um_per_px'] is None:
@@ -985,8 +989,15 @@ def analyze_endodyogeny(settings):
     df = df.dropna(subset=[settings['group_column']])
     df = _calculate_volume_bins(df, settings['compartment'], settings['min_area_bin'], settings['max_bins'], settings['verbose'])
     output['data'] = df
+    
+    
+    if settings['level'] == 'plate':
+        prc_column = 'plate'
+    else:
+        prc_column = 'prc'
+    
     # Perform chi-squared test and plot
-    results_df, pairwise_results_df, fig = plot_proportion_stacked_bars(settings, df, settings['group_column'], bin_column=f"{settings['compartment']}_volume_bin", level=settings['level'])
+    results_df, pairwise_results_df, fig = plot_proportion_stacked_bars(settings, df, settings['group_column'], bin_column=f"{settings['compartment']}_volume_bin", prc_column=prc_column, level=settings['level'], cmap=settings['cmap'])
     
     # Extract bin labels and indices for formatting the legend in the correct order
     bin_labels = df[f"{settings['compartment']}_volume_bin"].cat.categories if pd.api.types.is_categorical_dtype(df[f"{settings['compartment']}_volume_bin"]) else sorted(df[f"{settings['compartment']}_volume_bin"].unique())
@@ -1005,10 +1016,12 @@ def analyze_endodyogeny(settings):
         output_dir = os.path.join(settings['src'][0], 'results', 'analyze_endodyogeny')
         os.makedirs(output_dir, exist_ok=True)
         output_path = os.path.join(output_dir, 'chi_squared_results.csv')
+        output_path_data = os.path.join(output_dir, 'data.csv')
         output_path_pairwise = os.path.join(output_dir, 'chi_squared_results.csv')
         output_path_fig = os.path.join(output_dir, 'chi_squared_results.pdf')
         fig.savefig(output_path_fig, dpi=300, bbox_inches='tight')
         results_df.to_csv(output_path, index=False)
+        df.to_csv(output_path_data, index=False)
         pairwise_results_df.to_csv(output_path_pairwise, index=False)
         print(f"Chi-squared results saved to {output_path}")
         

{spacr-0.3.65 → spacr-0.3.66/spacr.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.3.65
+Version: 0.3.66
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson