fix: rel. intensity in chroms, bokeh marker size

also update snapshots accordingly
jcharkow · Jan 13, 2025 · bb0b6de · bb0b6de
1 parent 6dc3c8c
commit bb0b6de
Show file tree

Hide file tree

Showing 23 changed files with 14,832 additions and 14,828 deletions.
diff --git a/pyopenms_viz/_bokeh/core.py b/pyopenms_viz/_bokeh/core.py
@@ -413,7 +413,7 @@ def plot(self):
             )
 
         kwargs = dict(
-            size=self.marker_size,
+            size=self.marker_size / 4,  # divide so units similar to other backends
             line_width=0,
             fill_color=mapper if self.z is not None else self.current_color,
         )

diff --git a/pyopenms_viz/_core.py b/pyopenms_viz/_core.py
@@ -571,6 +571,10 @@ def __init__(self, data, config: ChromatogramConfig = None, **kwargs) -> None:
         else:
             self.data.sort_values(by=self.x, inplace=True)
 
+        # Convert to relative intensity if required
+        if self.relative_intensity:
+            self.data[self.y] = self.data[self.y] / self.data[self.y].max() * 100
+
         self.plot()
 
     def plot(self):

diff --git a/test/__snapshots__/test_chromatogram/test_chromatogram_plot[ms_bokeh-kwargs1].html b/test/__snapshots__/test_chromatogram/test_chromatogram_plot[ms_bokeh-kwargs1].html
diff --git a/test/__snapshots__/test_chromatogram/test_chromatogram_plot[ms_bokeh-kwargs2].html b/test/__snapshots__/test_chromatogram/test_chromatogram_plot[ms_bokeh-kwargs2].html
diff --git a/...snapshots__/test_chromatogram/test_chromatogram_plot[ms_matplotlib-kwargs2].png b/...snapshots__/test_chromatogram/test_chromatogram_plot[ms_matplotlib-kwargs2].png