Scatter widget

examples/scatter.py

@@ -0,0 +1,15 @@
+"""
+Scatter plots
+=============
+"""
+import napari
+
+viewer = napari.Viewer()
+viewer.open_sample("napari", "kidney")
+
+viewer.window.add_plugin_dock_widget(
+    plugin_name="napari-matplotlib", widget_name="Scatter"
+)
+
+if __name__ == "__main__":
+    napari.run()

src/napari_matplotlib/__init__.py

@@ -5,3 +5,4 @@
 
 
 from .histogram import *  # NoQA
+from .scatter import *  # NoQA

src/napari_matplotlib/base.py

@@ -8,6 +8,12 @@
 
 class NapariMPLWidget(QWidget):
     """
+    Base widget that can be embedded as a napari widget and contains a
+    Matplotlib canvas.
+
+    This creates a single Axes, and sub-classes should implement logic for
+    drawing on that Axes.
+
     Attributes
     ----------
     viewer : `napari.Viewer`
@@ -30,3 +36,10 @@ def __init__(self, napari_viewer: napari.viewer.Viewer):
 
         self.setLayout(QVBoxLayout())
         self.layout().addWidget(self.canvas)
+
+    @property
+    def current_z(self) -> int:
+        """
+        Current z-step of the viewer.
+        """
+        return self.viewer.dims.current_step[0]

src/napari_matplotlib/napari.yaml

@@ -6,6 +6,13 @@ contributions:
       python_name: napari_matplotlib:HistogramWidget
       title: Make a histogram
 
+    - id: napari-matplotlib.scatter
+      python_name: napari_matplotlib:ScatterWidget
+      title: Make a scatter plot
+
   widgets:
     - command: napari-matplotlib.histogram
       display_name: Histogram
+
+    - command: napari-matplotlib.scatter
+      display_name: Scatter

src/napari_matplotlib/scatter.py

@@ -0,0 +1,60 @@
+import matplotlib.colors as mcolor
+import napari
+
+from .base import NapariMPLWidget
+
+__all__ = ["ScatterWidget"]
+
+
+class ScatterWidget(NapariMPLWidget):
+    """
+    Widget to display scatter plot of two similarly shaped layers.
+
+    If there are more than 500 data points, a 2D histogram is displayed instead
+    of a scatter plot, to avoid too many scatter points.
+
+    Attributes
+    ----------
+    layers : list[`napari.layers.Layer`]
+        Current two layers being scattered.
+    """
+
+    def __init__(self, napari_viewer: napari.viewer.Viewer):
+        super().__init__(napari_viewer)
+        self.layers = self.viewer.layers[-2:]
+
+        self.viewer.dims.events.current_step.connect(
+            self.scatter_current_layers
+        )
+        self.viewer.layers.selection.events.changed.connect(self.update_layers)
+
+        self.scatter_current_layers()
+
+    def update_layers(self, event: napari.utils.events.Event) -> None:
+        """
+        Update the currently selected layers.
+        """
+        # Update current layer when selection changed in viewer
+        layers = self.viewer.layers.selection
+        if len(layers) == 2:
+            self.layers = list(layers)
+            self.scatter_current_layers()
+
+    def scatter_current_layers(self) -> None:
+        """
+        Clear the axes and scatter the currently selected layers.
+        """
+        self.axes.clear()
+        data = [layer.data[self.current_z] for layer in self.layers]
+        if data[0].size < 500:
+            self.axes.scatter(data[0], data[1], alpha=0.5)
+        else:
+            self.axes.hist2d(
+                data[0].ravel(),
+                data[1].ravel(),
+                bins=100,
+                norm=mcolor.LogNorm(),
+            )
+        self.axes.set_xlabel(self.layers[0].name)
+        self.axes.set_ylabel(self.layers[1].name)
+        self.canvas.draw()

src/napari_matplotlib/tests/test_scatter.py

@@ -0,0 +1,11 @@
+import numpy as np
+
+from napari_matplotlib import ScatterWidget
+
+
+def test_scatter(make_napari_viewer):
+    # Smoke test adding a histogram widget
+    viewer = make_napari_viewer()
+    viewer.add_image(np.random.random((100, 100)))
+    viewer.add_image(np.random.random((100, 100)))
+    ScatterWidget(viewer)