masster 0.4.3__py3-none-any.whl → 0.4.5__py3-none-any.whl

masster/study/plot.py

@@ -26,17 +26,17 @@ def _isolated_save_plot(plot_object, filename, abs_filename, logger, plot_title=
         # Use isolated file saving that doesn't affect global output state
         from bokeh.resources import Resources
         from bokeh.embed import file_html
-        
+
         # Create HTML content without affecting global state
         resources = Resources(mode='cdn')
         html = file_html(plot_object, resources, title=plot_title)
-        
+
         # Write directly to file
         with open(filename, 'w', encoding='utf-8') as f:
             f.write(html)
-        
+
         logger.info(f"Plot saved to: {abs_filename}")
-        
+
     elif filename.endswith(".png"):
         try:
             from bokeh.io.export import export_png
@@ -47,13 +47,13 @@ def _isolated_save_plot(plot_object, filename, abs_filename, logger, plot_title=
             html_filename = filename.replace('.png', '.html')
             from bokeh.resources import Resources
             from bokeh.embed import file_html
-            
+
             resources = Resources(mode='cdn')
             html = file_html(plot_object, resources, title=plot_title)
-            
+
             with open(html_filename, 'w', encoding='utf-8') as f:
                 f.write(html)
-                
+
             logger.warning(f"PNG export not available, saved as HTML instead: {html_filename}")
     elif filename.endswith(".pdf"):
         # Try to save as PDF, fall back to HTML if not available
@@ -66,25 +66,25 @@ def _isolated_save_plot(plot_object, filename, abs_filename, logger, plot_title=
             html_filename = filename.replace('.pdf', '.html')
             from bokeh.resources import Resources
             from bokeh.embed import file_html
-            
+
             resources = Resources(mode='cdn')
             html = file_html(plot_object, resources, title=plot_title)
-            
+
             with open(html_filename, 'w', encoding='utf-8') as f:
                 f.write(html)
-                
+
             logger.warning(f"PDF export not available, saved as HTML instead: {html_filename}")
     else:
         # Default to HTML for unknown extensions using isolated approach
         from bokeh.resources import Resources
         from bokeh.embed import file_html
-        
+
         resources = Resources(mode='cdn')
         html = file_html(plot_object, resources, title=plot_title)
-        
+
         with open(filename, 'w', encoding='utf-8') as f:
             f.write(html)
-            
+
         logger.info(f"Plot saved to: {abs_filename}")
 
 
@@ -97,28 +97,28 @@ def _isolated_show_notebook(plot_object):
     import holoviews as hv
     import warnings
     import logging
-    
+
     # Suppress both warnings and logging messages for the specific Bokeh callback warnings
     # that occur when Panel components with Python callbacks are converted to standalone Bokeh
     bokeh_logger = logging.getLogger('bokeh.embed.util')
     original_level = bokeh_logger.level
     bokeh_logger.setLevel(logging.ERROR)  # Suppress WARNING level messages
-    
+
     with warnings.catch_warnings():
         warnings.filterwarnings("ignore", message=".*standalone HTML/JS output.*", category=UserWarning)
         warnings.filterwarnings("ignore", message=".*real Python callbacks.*", category=UserWarning)
-        
+
         try:
             # First clear all output state
             reset_output()
-            
+
             # Set notebook mode
             output_notebook(hide_banner=True)
-            
-            # Reset Holoviews to notebook mode  
+
+            # Reset Holoviews to notebook mode
             hv.extension('bokeh', logo=False)
             hv.output(backend='bokeh', mode='jupyter')
-            
+
             # Show in notebook
             show(plot_object)
         finally:
@@ -129,16 +129,16 @@ def _isolated_show_notebook(plot_object):
 def _isolated_save_panel_plot(panel_obj, filename, abs_filename, logger, plot_title):
     """
     Save a Panel plot using isolated approach that doesn't affect global Bokeh state.
-    
+
     Args:
         panel_obj: Panel object to save
-        filename: Target filename 
+        filename: Target filename
         abs_filename: Absolute path for logging
         logger: Logger instance
         plot_title: Title for logging
     """
     import os  # Import os for path operations
-    
+
     if filename.endswith(".html"):
         # Panel save method should be isolated but let's be sure
         try:
@@ -147,7 +147,7 @@ def _isolated_save_panel_plot(panel_obj, filename, abs_filename, logger, plot_ti
             logger.info(f"{plot_title} saved to: {abs_filename}")
         except Exception as e:
             logger.error(f"Failed to save {plot_title}: {e}")
-            
+
     elif filename.endswith(".png"):
         try:
             from panel.io.save import save_png
@@ -164,7 +164,7 @@ def _isolated_save_panel_plot(panel_obj, filename, abs_filename, logger, plot_ti
                 logger.warning(f"PNG export not available, saved as HTML instead: {abs_html_filename}")
             except Exception as e:
                 logger.error(f"Failed to save {plot_title} as HTML fallback: {e}")
-                
+
     elif filename.endswith(".pdf"):
         # Try to save as PDF, fall back to HTML if not available
         try:
@@ -193,29 +193,29 @@ def _isolated_save_panel_plot(panel_obj, filename, abs_filename, logger, plot_ti
 def _isolated_show_panel_notebook(panel_obj):
     """
     Show a Panel plot in notebook with state isolation to prevent browser opening.
-    
+
     Args:
         panel_obj: Panel object to display
     """
     # Reset Bokeh state completely to prevent browser opening if output_file was called before
     from bokeh.io import reset_output, output_notebook
     import holoviews as hv
-    
+
     # First clear all output state
     reset_output()
-    
+
     # Set notebook mode
     output_notebook(hide_banner=True)
-    
-    # Reset Holoviews to notebook mode  
+
+    # Reset Holoviews to notebook mode
     hv.extension('bokeh', logo=False)
     hv.output(backend='bokeh', mode='jupyter')
-    
-    # For Panel objects in notebooks, use pn.extension and display inline
-    import panel as pn
+
+    # For Panel objects in notebooks, use on.extension and display inline
+    import panel as on
     try:
         # Configure Panel for notebook display
-        pn.extension('bokeh', inline=True, comms='vscode')
+        on.extension('bokeh', inline=True, comms='vscode')
         # Use IPython display to show inline instead of show()
         from IPython.display import display
         display(panel_obj)
@@ -278,25 +278,25 @@ def plot_alignment(
             # Create mapping from sample_uid to map_id and filter accordingly
             if hasattr(self, "samples_df") and self.samples_df is not None and not self.samples_df.is_empty():
                 samples_info = self.samples_df.to_pandas()
-                
+
                 # Filter samples_info to only selected sample_uids and get their map_ids
                 selected_samples = samples_info[samples_info["sample_uid"].isin(sample_uids)]
                 if selected_samples.empty:
                     self.logger.error("No matching samples found for the provided sample_uids.")
                     return
-                
+
                 # Get the map_ids for selected samples
                 selected_map_ids = selected_samples["map_id"].tolist()
-                
+
                 # Filter feature maps based on map_ids
                 filtered_maps = []
                 for map_id in selected_map_ids:
                     if 0 <= map_id < len(fmaps):
                         filtered_maps.append(fmaps[map_id])
-                
+
                 fmaps = filtered_maps
                 samples_info = selected_samples.reset_index(drop=True)
-                
+
                 if not fmaps:
                     self.logger.error("No feature maps found for the selected samples.")
                     return
@@ -438,7 +438,7 @@ def plot_alignment(
 
         # Use Polars instead of pandas
         features_df = self.features_df
-        
+
         # Filter by selected samples if specified
         if sample_uids is not None:
             features_df = features_df.filter(pl.col("sample_uid").is_in(sample_uids))
@@ -633,10 +633,10 @@ def plot_alignment(
         import os
         if not os.path.isabs(filename):
             filename = os.path.join(self.folder, filename)
-        
+
         # Convert to absolute path for logging
         abs_filename = os.path.abspath(filename)
-        
+
         # Use isolated file saving
         _isolated_save_plot(layout, filename, abs_filename, self.logger, "Alignment Plot")
     else:
@@ -864,10 +864,10 @@ def plot_consensus_2d(
         import os
         if not os.path.isabs(filename):
             filename = os.path.join(self.folder, filename)
-        
+
         # Convert to absolute path for logging
         abs_filename = os.path.abspath(filename)
-        
+
         # Use isolated file saving
         _isolated_save_plot(p, filename, abs_filename, self.logger, "Consensus 2D Plot")
     else:
@@ -1091,17 +1091,17 @@ def plot_samples_2d(
     # Only set legend properties if a legend was actually created to avoid Bokeh warnings
     if getattr(p, "legend", None) and len(p.legend) > 0:
         p.legend.visible = False
-    
+
     # Apply consistent save/display behavior
     if filename is not None:
         # Convert relative paths to absolute paths using study folder as base
         import os
         if not os.path.isabs(filename):
             filename = os.path.join(self.folder, filename)
-        
+
         # Convert to absolute path for logging
         abs_filename = os.path.abspath(filename)
-        
+
         # Use isolated file saving
         _isolated_save_plot(p, filename, abs_filename, self.logger, "Samples 2D Plot")
     else:
@@ -1132,7 +1132,7 @@ def plot_bpc(
     from bokeh.plotting import figure, show, output_file
     from bokeh.models import ColumnDataSource, HoverTool
     from bokeh.io.export import export_png
-    from masster.study.helpers import get_bpc
+    from master.study.helpers import get_bpc
 
     sample_uids = self._get_sample_uids(samples)
     if not sample_uids:
@@ -1271,10 +1271,10 @@ def plot_bpc(
         import os
         if not os.path.isabs(filename):
             filename = os.path.join(self.folder, filename)
-        
+
         # Convert to absolute path for logging
         abs_filename = os.path.abspath(filename)
-        
+
         # Use isolated file saving
         _isolated_save_plot(p, filename, abs_filename, self.logger, "BPC Plot")
     else:
@@ -1309,7 +1309,7 @@ def plot_eic(
     from bokeh.plotting import figure, show, output_file
     from bokeh.models import ColumnDataSource, HoverTool
     from bokeh.io.export import export_png
-    from masster.study.helpers import get_eic
+    from master.study.helpers import get_eic
 
     # Use study's eic_mz_tol parameter as default if not provided
     if mz_tol is None:
@@ -1442,10 +1442,10 @@ def plot_eic(
         import os
         if not os.path.isabs(filename):
             filename = os.path.join(self.folder, filename)
-        
+
         # Convert to absolute path for logging
         abs_filename = os.path.abspath(filename)
-        
+
         # Use isolated file saving
         _isolated_save_plot(p, filename, abs_filename, self.logger, "EIC Plot")
     else:
@@ -1595,10 +1595,10 @@ def plot_rt_correction(
         import os
         if not os.path.isabs(filename):
             filename = os.path.join(self.folder, filename)
-        
+
         # Convert to absolute path for logging
         abs_filename = os.path.abspath(filename)
-        
+
         # Use isolated file saving
         _isolated_save_plot(p, filename, abs_filename, self.logger, "RT Correction Plot")
     else:
@@ -1692,19 +1692,19 @@ def plot_chrom(
                     sorted_indices = np.argsort(rt)
                     rt = rt[sorted_indices]
                     inty = inty[sorted_indices]
-                    
+
                     # Get sample uid for this sample name
                     sample_uid = sample_name_to_uid.get(sample, None)
                     sample_color = color_map.get(sample, "#1f77b4")
-                    
+
                     # Create arrays with sample information for hover tooltips
                     sample_names_array = [sample] * len(rt)
                     sample_uids_array = [sample_uid] * len(rt)
                     sample_colors_array = [sample_color] * len(rt)
-                    
+
                     curve = hv.Curve(
-                        (rt, inty, sample_names_array, sample_uids_array, sample_colors_array), 
-                        kdims=["RT"], 
+                        (rt, inty, sample_names_array, sample_uids_array, sample_colors_array),
+                        kdims=["RT"],
                         vdims=["inty", "sample_name", "sample_uid", "sample_color"]
                     ).opts(
                         color=color_map[sample],
@@ -1775,17 +1775,17 @@ def plot_chrom(
     # stack vertically.
     # Stack all plots vertically in a Panel column
     layout = panel.Column(*[panel.panel(plot) for plot in plots])
-    
+
     # Apply consistent save/display behavior
     if filename is not None:
         # Convert relative paths to absolute paths using study folder as base
         import os
         if not os.path.isabs(filename):
             filename = os.path.join(self.folder, filename)
-        
+
         # Convert to absolute path for logging
         abs_filename = os.path.abspath(filename)
-        
+
         # Use isolated Panel saving
         _isolated_save_panel_plot(panel.panel(layout), filename, abs_filename, self.logger, "Chromatogram Plot")
     else:
@@ -2031,10 +2031,10 @@ def plot_consensus_stats(
         import os
         if not os.path.isabs(filename):
             filename = os.path.join(self.folder, filename)
-        
+
         # Convert to absolute path for logging
         abs_filename = os.path.abspath(filename)
-        
+
         # Use isolated file saving
         _isolated_save_plot(grid, filename, abs_filename, self.logger, "Consensus Stats Plot")
     else:
@@ -2097,7 +2097,7 @@ def plot_pca(
 
     # Extract only the sample columns (exclude consensus_uid column)
     sample_cols = [col for col in consensus_matrix.columns if col != "consensus_uid"]
-    
+
     # Convert consensus matrix to numpy, excluding the consensus_uid column
     if hasattr(consensus_matrix, "select"):
         # Polars DataFrame
@@ -2295,10 +2295,10 @@ def plot_pca(
         import os
         if not os.path.isabs(filename):
             filename = os.path.join(self.folder, filename)
-        
+
         # Convert to absolute path for logging
         abs_filename = os.path.abspath(filename)
-        
+
         # Use isolated file saving
         _isolated_save_plot(p, filename, abs_filename, self.logger, "PCA Plot")
     else:
@@ -2325,7 +2325,7 @@ def plot_tic(
     from bokeh.plotting import figure, show, output_file
     from bokeh.models import ColumnDataSource, HoverTool
     from bokeh.io.export import export_png
-    from masster.study.helpers import get_tic
+    from master.study.helpers import get_tic
 
     sample_uids = self._get_sample_uids(samples)
     if not sample_uids:
@@ -2449,10 +2449,10 @@ def plot_tic(
         import os
         if not os.path.isabs(filename):
             filename = os.path.join(self.folder, filename)
-        
+
         # Convert to absolute path for logging
         abs_filename = os.path.abspath(filename)
-        
+
         # Use isolated file saving
         _isolated_save_plot(p, filename, abs_filename, self.logger, "TIC Plot")
     else: