masster 0.4.19__py3-none-any.whl → 0.4.20__py3-none-any.whl

masster/study/plot.py

@@ -512,9 +512,9 @@ def plot_consensus_2d(
     filename=None,
     colorby="number_samples",
     cmap=None,
-    markersize=4,
+    markersize=8,
     sizeby="inty_mean",
-    scaling="dynamic",
+    scaling="static",
     alpha=0.7,
     width=600,
     height=450,
@@ -529,7 +529,7 @@ def plot_consensus_2d(
         colorby (str): Column name to use for color mapping (default: "number_samples")
         sizeby (str): Column name to use for size mapping (default: "inty_mean")
         markersize (int): Base marker size (default: 6)
-        size (str): Controls whether points scale with zoom. Options:
+        scaling (str): Controls whether points scale with zoom. Options:
                    'dynamic' - points use circle() and scale with zoom
                    'static' - points use scatter() and maintain fixed pixel size
         alpha (float): Transparency level (default: 0.7)
@@ -553,7 +553,7 @@ def plot_consensus_2d(
     if colorby not in data.columns:
         self.logger.error(f"Column {colorby} not found in consensus_df.")
         return
-    if sizeby not in data.columns:
+    if sizeby is not None and sizeby not in data.columns:
         self.logger.warning(f"Column {sizeby} not found in consensus_df.")
         sizeby = None
     # if sizeby is not None, set markersize to sizeby
@@ -673,10 +673,16 @@ def plot_consensus_2d(
     p.yaxis.axis_label = "m/z"
     scatter_renderer: Any = None
     if scaling.lower() in ["dyn", "dynamic"]:
+        # Calculate appropriate radius for dynamic scaling based on data range
+        rt_range = data["rt"].max() - data["rt"].min()
+        mz_range = data["mz"].max() - data["mz"].min()
+        # Use a fraction of the smaller dimension for radius, similar to sample plotting
+        dynamic_radius = min(rt_range, mz_range) * 0.0005 * markersize
+        
         scatter_renderer = p.circle(
             x="rt",
             y="mz",
-            radius=markersize,
+            radius=dynamic_radius,
             fill_color={"field": colorby, "transform": color_mapper},
             line_color=None,
             alpha=alpha,

masster/study/study.py

@@ -120,7 +120,10 @@ from masster.study.merge import merge
 from masster.study.merge import _reset_consensus_data
 from masster.study.merge import _extract_consensus_features
 from masster.study.merge import _perform_adduct_grouping
+from masster.study.merge import _consensus_cleanup
+from masster.study.merge import _identify_adduct_by_mass_shift
 from masster.study.merge import _finalize_merge
+from masster.study.merge import _count_tight_clusters
 from masster.study.processing import integrate
 from masster.study.processing import find_ms2
 from masster.study.parameters import store_history
@@ -496,6 +499,8 @@ class Study:
     _reset_consensus_data = _reset_consensus_data
     _extract_consensus_features = _extract_consensus_features
     _perform_adduct_grouping = _perform_adduct_grouping
+    _consensus_cleanup = _consensus_cleanup
+    _identify_adduct_by_mass_shift = _identify_adduct_by_mass_shift
     _finalize_merge = _finalize_merge
     
     # === Default Parameters ===
@@ -873,6 +878,15 @@ class Study:
             + (self.consensus_mapping_df.estimated_size() if self.consensus_mapping_df is not None else 0)
         )
 
+        # Calculate tight clusters count
+        tight_clusters_count = 0
+        if consensus_df_len > 0:
+            try:
+                tight_clusters_count = _count_tight_clusters(self, mz_tol=0.04, rt_tol=0.3)
+            except Exception as e:
+                # If tight clusters calculation fails, just use 0
+                tight_clusters_count = 0
+
         # Add warning symbols for out-of-range values
         consensus_warning = f" {_WARNING_SYMBOL}" if consensus_df_len < 50 else ""
 
@@ -901,6 +915,9 @@ class Study:
             elif max_samples < samples_df_len * 0.8:
                 max_samples_warning = f" {_WARNING_SYMBOL}"
 
+        # Add warning for tight clusters
+        tight_clusters_warning = f" {_WARNING_SYMBOL}" if tight_clusters_count > 10 else ""
+
         summary = (
             f"Study folder:           {self.folder}\n"
             f"Last save:              {self.filename}\n"
@@ -910,6 +927,7 @@ class Study:
             f"- not in consensus:     {ratio_not_in_consensus_to_total:.0f}%\n"
             f"Consensus:              {consensus_df_len}{consensus_warning}\n"
             f"- RT spread:            {rt_spread_text}{rt_spread_warning}\n"
+            f"- Tight clusters:       {tight_clusters_count}{tight_clusters_warning}\n"
             f"- Min samples count:    {min_samples:.0f}\n"
             f"- Mean samples count:   {mean_samples:.0f}\n"
             f"- Max samples count:    {max_samples:.0f}{max_samples_warning}\n"

masster/wizard/__init__.py

@@ -4,8 +4,11 @@ Wizard module for automated processing of mass spectrometry studies.
 This module provides the Wizard class for fully automated processing of MS data
 from raw files to final study results, including batch conversion, assembly,
 alignment, merging, plotting, and export.
+
+The create_script() function allows immediate generation of standalone analysis
+scripts without creating a Wizard instance first.
 """
 
-from .wizard import Wizard, wizard_def
+from .wizard import Wizard, wizard_def, create_script
 
-__all__ = ["Wizard", "wizard_def"]
+__all__ = ["Wizard", "wizard_def", "create_script"]