Merge pull request #20 from singjc/add/3d_peakmap

Add/3d peakmap

Author: singjc

nbs/PeakMap.ipynb

@@ -210,7 +210,7 @@ class BOKEHLinePlot(BOKEHPlot, LinePlot):
 
     @classmethod
     @APPEND_PLOT_DOC
-    def plot(cls, fig, data, x, y, by: str | None = None, **kwargs):
+    def plot(cls, fig, data, x, y, by: str | None = None, plot_3d=False, **kwargs):
         """
         Plot a line plot
         """
@@ -219,7 +219,7 @@ def plot(cls, fig, data, x, y, by: str | None = None, **kwargs):
         if by is None:
             source = ColumnDataSource(data)
             if color_gen is not None:
-                kwargs["line_color"] = next(color_gen)
+                kwargs["line_color"] = color_gen if isinstance(color_gen, str) else next(color_gen)
             line = fig.line(x=x, y=y, source=source, **kwargs)
 
             return fig, None
@@ -229,7 +229,7 @@ def plot(cls, fig, data, x, y, by: str | None = None, **kwargs):
             for group, df in data.groupby(by):
                 source = ColumnDataSource(df)
                 if color_gen is not None:
-                    kwargs["line_color"] = next(color_gen)
+                    kwargs["line_color"] = color_gen if isinstance(color_gen, str) else next(color_gen)
                 line = fig.line(x=x, y=y, source=source, **kwargs)
                 legend_items.append((group, [line]))
 
@@ -245,30 +245,17 @@ class BOKEHVLinePlot(BOKEHPlot, VLinePlot):
 
     @classmethod
     @APPEND_PLOT_DOC
-    def plot(cls, fig, data, x, y, by: str | None = None, **kwargs):
+    def plot(cls, fig, data, x, y, by: str | None = None, plot_3d=False, **kwargs):
         """
         Plot a set of vertical lines
         """
         color_gen = kwargs.pop("line_color", None)
         if color_gen is None:
             color_gen = ColorGenerator()
         data["line_color"] = [next(color_gen) for _ in range(len(data))]
-        if by is None:
-            source = ColumnDataSource(data)
-            line = fig.segment(
-                x0=x,
-                y0=0,
-                x1=x,
-                y1=y,
-                source=source,
-                line_color="line_color",
-                **kwargs,
-            )
-            return fig, None
-        else:
-            legend_items = []
-            for group, df in data.groupby(by):
-                source = ColumnDataSource(df)
+        if not plot_3d:
+            if by is None:
+                source = ColumnDataSource(data)
                 line = fig.segment(
                     x0=x,
                     y0=0,
@@ -278,11 +265,27 @@ def plot(cls, fig, data, x, y, by: str | None = None, **kwargs):
                     line_color="line_color",
                     **kwargs,
                 )
-                legend_items.append((group, [line]))
-
-            legend = Legend(items=legend_items)
-
-            return fig, legend
+                return fig, None
+            else:
+                legend_items = []
+                for group, df in data.groupby(by):
+                    source = ColumnDataSource(df)
+                    line = fig.segment(
+                        x0=x,
+                        y0=0,
+                        x1=x,
+                        y1=y,
+                        source=source,
+                        line_color="line_color",
+                        **kwargs,
+                    )
+                    legend_items.append((group, [line]))
+
+                legend = Legend(items=legend_items)
+        
+                return fig, legend
+        else:
+            raise NotImplementedError("3D Vline plots are not supported in Bokeh")
 
     def _add_annotations(
         self,
@@ -312,7 +315,7 @@ class BOKEHScatterPlot(BOKEHPlot, ScatterPlot):
 
     @classmethod
     @APPEND_PLOT_DOC
-    def plot(cls, fig, data, x, y, by: str | None = None, **kwargs):
+    def plot(cls, fig, data, x, y, by: str | None = None, plot_3d=False, **kwargs):
         """
         Plot a scatter plot
         """
@@ -466,16 +469,19 @@ class BOKEHPeakMapPlot(BOKEH_MSPlot, PeakMapPlot):
     """
 
     def create_main_plot(self, x, y, z, class_kwargs, other_kwargs):
-        scatterPlot = self.get_scatter_renderer(self.data, x, y, **class_kwargs)
+        if not self.plot_3d:
+            scatterPlot = self.get_scatter_renderer(self.data, x, y, **class_kwargs)
 
-        self.fig = scatterPlot.generate(z=z, **other_kwargs)
+            self.fig = scatterPlot.generate(z=z, **other_kwargs)
 
-        if self.annotation_data is not None:
-            self._add_box_boundaries(self.annotation_data)
+            if self.annotation_data is not None:
+                self._add_box_boundaries(self.annotation_data)
 
-        tooltips, _ = self._create_tooltips({self.xlabel: x, self.ylabel: y, "intensity": z})
+            tooltips, _ = self._create_tooltips({self.xlabel: x, self.ylabel: y, "intensity": z})
 
-        self._add_tooltips(self.fig, tooltips)
+            self._add_tooltips(self.fig, tooltips)
+        else:
+            raise NotImplementedError("3D PeakMap plots are not supported in Bokeh")
 
     def create_x_axis_plot(self, x, z, class_kwargs):
         x_fig = super().create_x_axis_plot(x, z, class_kwargs)

nbs/pyopenms_viz_tutorial.ipynb

@@ -178,6 +178,7 @@ def default_legend_factory():
     title: str = "1D Plot"
     xlabel: str = "X-axis"
     ylabel: str = "Y-axis"
+    zlabel: str = "Z-axis"
     x_axis_location: str = "below"
     y_axis_location: str = "left"
     min_border: str = 0
@@ -231,6 +232,7 @@ def set_plot_labels(self):
                 "title": "PeakMap",
                 "xlabel": "Retention Time",
                 "ylabel": "mass-to-charge",
+                "zlabel": "Intensity",
             },
             # Add more plot types as needed
         }
@@ -239,6 +241,8 @@ def set_plot_labels(self):
             self.title = plot_configs[self.kind]["title"]
             self.xlabel = plot_configs[self.kind]["xlabel"]
             self.ylabel = plot_configs[self.kind]["ylabel"]
+            if self.kind == "peakmap":
+                self.zlabel = plot_configs[self.kind]["zlabel"]
 
             if self.relative_intensity and "Intensity" in self.ylabel:
                 self.ylabel = "Relative " + self.ylabel

pyopenms_viz/_bokeh/core.py

@@ -108,6 +108,7 @@ def __init__(
         z: str | None = None,
         kind=None,
         by: str | None = None,
+        plot_3d: bool = False,
         relative_intensity: bool = False,
         subplots: bool | None = None,
         sharex: bool | None = None,
@@ -120,6 +121,7 @@ def __init__(
         title: str | None = None,
         xlabel: str | None = None,
         ylabel: str | None = None,
+        zlabel: str | None = None,
         x_axis_location: str | None = None,
         y_axis_location: str | None = None,
         line_type: str | None = None,
@@ -136,6 +138,7 @@ def __init__(
         self.data = data.copy()
         self.kind = kind
         self.by = by
+        self.plot_3d = plot_3d
         self.relative_intensity = relative_intensity
 
         # Plotting attributes
@@ -150,6 +153,7 @@ def __init__(
         self.title = title
         self.xlabel = xlabel
         self.ylabel = ylabel
+        self.zlabel = zlabel
         self.x_axis_location = x_axis_location
         self.y_axis_location = y_axis_location
         self.line_type = line_type
@@ -298,7 +302,7 @@ def _make_plot(self, fig, **kwargs) -> None:
         tooltips = kwargs.pop("tooltips", None)
         custom_hover_data = kwargs.pop("custom_hover_data", None)
 
-        newlines, legend = self.plot(fig, self.data, self.x, self.y, self.by, **kwargs)
+        newlines, legend = self.plot(fig, self.data, self.x, self.y, self.by, self.plot_3d, **kwargs)
 
         if legend is not None:
             self._add_legend(newlines, legend)
@@ -308,7 +312,7 @@ def _make_plot(self, fig, **kwargs) -> None:
             self._add_tooltips(newlines, tooltips, custom_hover_data)
 
     @abstractmethod
-    def plot(cls, fig, data, x, y, by: str | None = None, **kwargs):
+    def plot(cls, fig, data, x, y, by: str | None = None, plot_3d: bool = False, **kwargs):
         """
         Create the plot
         """
@@ -491,7 +495,11 @@ def plot(self, data, x, y, **kwargs):
         """
         Create the plot
         """
-        color_gen = ColorGenerator()
+        if 'line_color' not in kwargs:
+            color_gen = ColorGenerator()
+        else:
+            color_gen = kwargs['line_color']
+        
         tooltip_entries = {"retention time": x, "intensity": y}
         if "Annotation" in self.data.columns:
             tooltip_entries["annotation"] = "Annotation"
@@ -795,6 +803,7 @@ def __init__(
         num_x_bins: int = 50,
         num_y_bins: int = 50,
         z_log_scale: bool = False,
+        # plot_3d: bool = False,
         **kwargs,
     ) -> None:
         # Copy data since it will be modified
@@ -826,13 +835,23 @@ def __init__(
         ):
             data[x] = cut(data[x], bins=num_x_bins)
             data[y] = cut(data[y], bins=num_y_bins)
-
-            # Group by x and y bins and calculate the mean intensity within each bin
-            data = (
-                data.groupby([x, y], observed=True)
-                .agg({z: "mean"})
-                .reset_index()
-            )
+            by = kwargs.pop("by", None)
+            if by is not None:
+                # Group by x, y and by columns and calculate the mean intensity within each bin
+                data = (
+                    data.groupby([x, y, by], observed=True)
+                    .agg({z: "mean"})
+                    .reset_index()
+                )
+                # Add by back to kwargs
+                kwargs["by"] = by
+            else:
+                # Group by x and y bins and calculate the mean intensity within each bin
+                data = (
+                    data.groupby([x, y], observed=True)
+                    .agg({z: "mean"})
+                    .reset_index()
+                )
             data[x] = data[x].apply(lambda interval: interval.mid).astype(float)
             data[y] = data[y].apply(lambda interval: interval.mid).astype(float)
             data = data.fillna(0)
@@ -846,7 +865,11 @@ def __init__(
 
         super().__init__(data, x, y, z=z, **kwargs)
 
+        # if not plot_3d:
         self.plot(x, y, z, **kwargs)
+        # else:
+        #     self.plot_3d(x, y, z, **kwargs)
+            
         if self.show_plot:
             self.show()
 
@@ -873,6 +896,12 @@ def plot(self, x, y, z, **kwargs):
             y_fig = self.create_y_axis_plot(y, z, class_kwargs_copy)
 
             self.combine_plots(x_fig, y_fig)
+    
+    # def plot_3d(self, x, y, z, **kwargs):
+    #     class_kwargs, other_kwargs = self._separate_class_kwargs(**kwargs)
+        
+    #     self.create_main_plot_3d(x, y, z, class_kwargs, other_kwargs)
+    #     pass
 
     @staticmethod
     def _integrate_data_along_dim(
@@ -896,6 +925,10 @@ def create_main_plot(self, x, y, z, class_kwargs, other_kwargs):
     # by default the main plot with marginals is plotted the same way as the main plot unless otherwise specified
     def create_main_plot_marginals(self, x, y, z, class_kwargs, other_kwargs):
         self.create_main_plot(x, y, z, class_kwargs, other_kwargs)
+        
+    # @abstractmethod
+    # def create_main_plot_3d(self, x, y, z, class_kwargs, other_kwargs):
+    #     pass
 
     @abstractmethod
     def create_x_axis_plot(self, x, z, class_kwargs) -> "figure":
@@ -1006,6 +1039,7 @@ def __call__(self, *args: Any, **kwargs: Any) -> Any:
         # Call the plot method of the selected backend
         if "backend" in kwargs:
             kwargs.pop("backend")
+        
         return plot_backend.plot(self._parent, x=x, y=y, kind=kind, **kwargs)
 
     @staticmethod