Merge branch 'main' of github.com:OpenMS/pyopenms_viz

Author: singjc

README.md

@@ -22,7 +22,7 @@ The recommended way of installing pyopenms_viz is through the Python Package Ind
 First create a new environemnt:
 
 ```bash
-conda create --name=massdash python=3.10
+conda create --name=pyopenms_viz python=3.10
 conda activate pyopenms_viz 
 ```
 Then in the new environment install pyopenms_viz.

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