Merge pull request #100 from Roestlab/patch/peak_boundary_int

Patch/peak boundary int
Roestlab · Jan 25, 2024 · 7560d19 · 7560d19
2 parents aa27f47 + f27fad7
commit 7560d19
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Showing 9 changed files with 94 additions and 1,643 deletions.
diff --git a/docs/python_docs/Advanced Plotting.ipynb b/docs/python_docs/Advanced Plotting.ipynb
diff --git a/docs/python_docs/Plotting1D.ipynb b/docs/python_docs/Plotting1D.ipynb
diff --git a/manuscript/main_figures/Figure-3-Features-Comparison.ipynb b/manuscript/main_figures/Figure-3-Features-Comparison.ipynb
diff --git a/manuscript/main_figures/Figure-4-Extraction-Optimization.ipynb b/manuscript/main_figures/Figure-4-Extraction-Optimization.ipynb
diff --git a/manuscript/main_figures/Figure-5-Peak-Picking-Demonstration.ipynb b/manuscript/main_figures/Figure-5-Peak-Picking-Demonstration.ipynb
diff --git a/massdash/loaders/GenericLoader.py b/massdash/loaders/GenericLoader.py
@@ -178,11 +178,7 @@ def plotChromatogram(self,
         plotter = InteractivePlotter(pc)
 
         # Plot the chromatogram data
-        print(transitionGroup)
-        fig = plotter.plot(transitionGroup)
-
-        # Add boundaries to the plot
-        fig = plotter.add_peak_boundaries(fig, transitionGroupFeatures)
+        fig = plotter.plot(transitionGroup, transitionGroupFeatures)
 
         show(fig)
 

diff --git a/massdash/plotting/GenericPlotter.py b/massdash/plotting/GenericPlotter.py
@@ -57,6 +57,7 @@ def __init__(self):
         self.type_of_comparison = "retention time vs ion mobility"
         self.context = "streamlit" # or "jupyter"
         self.normalization_dict = {'type':'none'} # or {'type':'equalization', 'bins': (int)}
+        self.ms_level_str = 'ms1ms2'
 
     def __str__(self):
         return f"{'-'*8} PlotConfig {'-'*8}\ninclude_ms1: {self.include_ms1}\ninclude_ms2: {self.include_ms2}\nnum_plot_columns: {self.num_plot_columns}\ntitle: {self.title}\nsubtitle: {self.subtitle}\nx_axis_label: {self.x_axis_label}\ny_axis_label: {self.y_axis_label}\nsmoothing_dict: {self.smoothing_dict}\nx_range: {self.x_range}\ny_range: {self.y_range}\nscale_intensity: {self.scale_intensity}\naggregate_mslevels: {self.aggregate_mslevels}\ntype_of_heatmap: {self.type_of_heatmap}\ntype_of_3d_plot: {self.type_of_3d_plot}\ntype_of_comparison: {self.type_of_comparison}\n{'-'*30}"
@@ -71,6 +72,13 @@ def update(self, config_dict):
         for key, value in config_dict.items():
             if hasattr(self, key):
                 setattr(self, key, value)
+
+        if self.include_ms1 and self.include_ms2:
+            self.ms_level_str = 'ms1ms2'
+        elif self.include_ms1 and not self.include_ms2:
+            self.ms_level_str = 'ms1'
+        elif not self.include_ms1 and self.include_ms2:
+            self.ms_level_str = 'ms2'
 
 class GenericPlotter(ABC):
     """ 
@@ -89,7 +97,8 @@ def __init__(self, config: PlotConfig):
         self.y_range = config.y_range
         self.scale_intensity = config.scale_intensity
         self.normalization_dict = config.normalization_dict
-
+        self.ms_level_str = config.ms_level_str
+
     @abstractmethod
     def plot(self, transitionGroup: TransitionGroup, features: Optional[List[TransitionGroupFeature]] = None, plot_type: Literal['chromatogram', 'mobilogram', 'spectrum'] = 'chromatogram'):
         pass

diff --git a/massdash/plotting/InteractivePlotter.py b/massdash/plotting/InteractivePlotter.py
@@ -47,7 +47,7 @@ def __init__(self, config: PlotConfig, verbose: bool=False):
         else:
             LOGGER.setLevel("INFO")
 
-    def plot(self, transitionGroup: TransitionGroup, features: Optional[List[TransitionGroupFeature]] = None, plot_type: Literal['chromatogram', 'mobilogram', 'spectra'] = 'chromatogram') -> figure:
+    def plot(self, transitionGroup: TransitionGroup, features: Optional[List[TransitionGroupFeature]] = None, plot_type: Literal['chromatogram', 'mobilogram', 'spectrum'] = 'chromatogram', feature_legend_labels:Optional[List[str]] = []) -> figure:
         """
         Plots the given transitionGroup using the specified plot type.
 
@@ -60,10 +60,10 @@ def plot(self, transitionGroup: TransitionGroup, features: Optional[List[Transit
             figure: The generated plot as a Bokeh figure object.
         """
         if plot_type == 'chromatogram':
-            plot =  self.plot_chromatogram(transitionGroup, features)
+            plot =  self.plot_chromatogram(transitionGroup, features, feature_legend_labels)
         elif plot_type == 'mobilogram':
             plot =  self.plot_mobilogram(transitionGroup)
-        elif plot_type == 'spectra':
+        elif plot_type == 'spectrum':
             plot =  self.plot_spectra(transitionGroup)
         else:
             raise ValueError("Unsupported plot plot_type")
@@ -148,13 +148,18 @@ def process_chrom(self, p: figure, chrom: Chromatogram, label: str, color: str='
 
         return line
 
-    def add_peak_boundaries(self, p: figure, features: List[TransitionGroupFeature], legend_labels:Optional[List[str]] = []) -> None:
+    def __add_peak_boundaries(self, 
+                            p: figure, 
+                            features: List[TransitionGroupFeature],
+                            transitionGroup: TransitionGroup,
+                            legend_labels:Optional[List[str]] = []) -> None:
         """
         Adds peak boundaries to a Bokeh figure.
 
         Args:
             p (figure): The Bokeh figure to add the peak boundaries to.
             features (List[TransitionGroupFeature]): A list of peak features to highlight on the plot.
+            transitionGroup (TransitionGroup): The TransitionGroup object containing precursor and transition data.
             legend_labels (List[str], optional): A list of labels for the peak features. Defaults to [].
         """
         if len(features) <= 8:
@@ -182,7 +187,7 @@ def add_peak_boundaries(self, p: figure, features: List[TransitionGroupFeature],
                     'bottom_int'    : [0]})
             else:
                 source = ColumnDataSource(data = {
-                    'Intensity' : [feature.areaIntensity],
+                    'Intensity' : [transitionGroup.max((feature.leftBoundary, feature.rightBoundary), level=self.ms_level_str)],
                     'leftWidth'   : [feature.leftBoundary],
                     'rightWidth'   : [feature.rightBoundary],
                     'ms2_mscore' : [feature.qvalue],
@@ -221,7 +226,7 @@ def add_peak_boundaries(self, p: figure, features: List[TransitionGroupFeature],
 
         return p
 
-    def plot_chromatogram(self, transitionGroup: TransitionGroup, features: Optional[List[TransitionGroupFeature]]) -> figure:
+    def plot_chromatogram(self, transitionGroup: TransitionGroup, features: Optional[List[TransitionGroupFeature]], feature_legend_labels:Optional[List[str]] = []) -> figure:
         """
         Plots a chromatogram for a given TransitionGroup.
 
@@ -323,7 +328,7 @@ def plot_chromatogram(self, transitionGroup: TransitionGroup, features: Optional
 
         # Add peak boundaries if available
         if features is not None:
-            p = self.add_peak_boundaries(p, features)
+            p = self.__add_peak_boundaries(p, features, transitionGroup, feature_legend_labels)
 
         return p
 

diff --git a/massdash/structs/TransitionGroup.py b/massdash/structs/TransitionGroup.py
@@ -208,12 +208,6 @@ def plot(self,
 
         plotter = InteractivePlotter(config)
 
-        plotter.plot(self)
-
-        if transitionGroupFeatures is not None:
-            if self.dataType == Chromatogram:
-                plotter.add_peak_boundaries(plotter.fig, transitionGroupFeatures)
-            else:
-                raise NotImplementedError("Peak boundaries are only implemented for chromatograms")
+        plotter.plot(self, transitionGroupFeatures, config.plot_type)
 
         plotter.show()