[ENH] Scatterplot: indicate overlap of points.

Orange/widgets/unsupervised/owmds.py

@@ -56,6 +56,12 @@ def update_data(self, attr_x, attr_y, reset_view=True):
         self.plot_widget.setAspectLocked(True, 1)
 
     def compute_sizes(self):
+        """Handle 'Stress' size option.
+        Everything else is passed to Scatterplot's compute_sizes"""
+
+        if self.attr_size != "Stress":
+            return super().compute_sizes()
+
         def scale(a):
             dmin, dmax = np.nanmin(a), np.nanmax(a)
             if dmax - dmin > 0:
@@ -64,17 +70,8 @@ def scale(a):
                 return np.zeros_like(a)
 
         self.master.Information.missing_size.clear()
-        if self.attr_size is None:
-            size_data = np.full((self.n_points,), self.point_width,
-                                dtype=float)
-        elif self.attr_size == "Stress":
-            size_data = scale(stress(self.master.embedding, self.master.effective_matrix))
-            size_data = self.MinShapeSize + size_data * self.point_width
-        else:
-            size_data = \
-                self.MinShapeSize + \
-                self.scaled_data.get_column_view(self.attr_size)[0][self.valid_data] * \
-                self.point_width
+        size_data = scale(stress(self.master.embedding, self.master.effective_matrix))
+        size_data = self.MinShapeSize + size_data * self.point_width
         nans = np.isnan(size_data)
         if np.any(nans):
             size_data[nans] = self.MinShapeSize - 2

Orange/widgets/utils/plot/owplotgui.py

@@ -465,11 +465,14 @@ def __init__(self, plot):
         self.shape_model = DomainModel(placeholder="(Same shape)",
                                        valid_types=DiscreteVariable)
         self.size_model = DomainModel(placeholder="(Same size)",
+                                      order=(self.SizeByOverlap,) + DomainModel.SEPARATED,
                                       valid_types=ContinuousVariable)
         self.label_model = DomainModel(placeholder="(No labels)")
         self.points_models = [self.color_model, self.shape_model,
                               self.size_model, self.label_model]
 
+    SizeByOverlap = "Overlap"
+
     Spacing = 0
 
     ShowLegend = 2

Orange/widgets/visualize/owscatterplotgraph.py

@@ -1,8 +1,8 @@
-from collections import Counter
+from collections import Counter, defaultdict
 import sys
 import itertools
 from xml.sax.saxutils import escape
-from math import log10, floor, ceil
+from math import log2, log10, floor, ceil
 
 import numpy as np
 from scipy.stats import linregress
@@ -691,13 +691,13 @@ def update_data(self, attr_x, attr_y, reset_view=True):
                 self.shown_x.name, self.shown_y.name)
             return
 
-        x_data, y_data = self.get_xy_data_positions(
+        self.x_data, self.y_data = self.get_xy_data_positions(
             attr_x, attr_y, self.valid_data)
-        self.n_points = len(x_data)
+        self.n_points = len(self.x_data)
 
         if reset_view:
-            min_x, max_x = np.nanmin(x_data), np.nanmax(x_data)
-            min_y, max_y = np.nanmin(y_data), np.nanmax(y_data)
+            min_x, max_x = np.nanmin(self.x_data), np.nanmax(self.x_data)
+            min_y, max_y = np.nanmin(self.y_data), np.nanmax(self.y_data)
             self.view_box.setRange(
                 QRectF(min_x, min_y, max_x - min_x, max_y - min_y),
                 padding=0.025)
@@ -712,6 +712,15 @@ def update_data(self, attr_x, attr_y, reset_view=True):
             else:
                 self.set_labels(axis, None)
 
+        # compute overlaps of points for use in compute_colors and compute_sizes
+        self.overlaps = []
+        self.coord_to_id = defaultdict(list)
+        for i, xy in enumerate(zip(self.x_data, self.y_data)):
+            self.coord_to_id[xy].append(i)
+        self.overlaps = [len(self.coord_to_id[xy])
+                         for i, xy in enumerate(zip(self.x_data, self.y_data))]
+        self.overlap_factor = [1+log2(o) for o in self.overlaps]
+
         color_data, brush_data = self.compute_colors()
         color_data_sel, brush_data_sel = self.compute_colors_sel()
         size_data = self.compute_sizes()
@@ -721,7 +730,7 @@ def update_data(self, attr_x, attr_y, reset_view=True):
             rgb_data = [pen.color().getRgb()[:3] for pen in color_data]
             self.density_img = classdensity.class_density_image(
                 min_x, max_x, min_y, max_y, self.resolution,
-                x_data, y_data, rgb_data)
+                self.x_data, self.y_data, rgb_data)
             self.plot_widget.addItem(self.density_img)
 
         self.data_indices = np.flatnonzero(self.valid_data)
@@ -730,11 +739,11 @@ def update_data(self, attr_x, attr_y, reset_view=True):
                 self.shown_x.name, self.shown_y.name)
 
         self.scatterplot_item = ScatterPlotItem(
-            x=x_data, y=y_data, data=self.data_indices,
+            x=self.x_data, y=self.y_data, data=self.data_indices,
             symbol=shape_data, size=size_data, pen=color_data, brush=brush_data
         )
         self.scatterplot_item_sel = ScatterPlotItem(
-            x=x_data, y=y_data, data=self.data_indices,
+            x=self.x_data, y=self.y_data, data=self.data_indices,
             symbol=shape_data, size=size_data + SELECTION_WIDTH,
             pen=color_data_sel, brush=brush_data_sel
         )
@@ -803,7 +812,7 @@ def set_axis_title(self, axis, title):
 
     def compute_sizes(self):
         self.master.Information.missing_size.clear()
-        if self.attr_size is None:
+        if self.attr_size in [None, OWPlotGUI.SizeByOverlap]:
             size_data = np.full((self.n_points,), self.point_width,
                                 dtype=float)
         else:
@@ -815,6 +824,11 @@ def compute_sizes(self):
         if np.any(nans):
             size_data[nans] = self.MinShapeSize - 2
             self.master.Information.missing_size(self.attr_size)
+
+        # scale sizes because of overlaps
+        if self.attr_size == OWPlotGUI.SizeByOverlap:
+            size_data = np.multiply(size_data, self.overlap_factor)
+
         return size_data
 
     def update_sizes(self):
@@ -947,16 +961,26 @@ def compute_colors(self, keep_colors=False):
                 c_data = c_data.astype(int)
                 colors = np.r_[palette.getRGB(np.arange(n_colors)),
                                [[128, 128, 128]]]
-                pens = np.array(
+                pen_colors_palette = np.array(
                     [_make_pen(QColor(*col).darker(self.DarkerValue), 1.5)
                      for col in colors])
-                self.pen_colors = pens[c_data]
+                self.pen_colors = pen_colors_palette[c_data]
                 alpha = self.alpha_value if subset is None else 255
-                self.brush_colors = np.array([
+                brush_colors_palette = np.array([
                     [QBrush(QColor(0, 0, 0, 0)),
                      QBrush(QColor(col[0], col[1], col[2], alpha))]
                     for col in colors])
-                self.brush_colors = self.brush_colors[c_data]
+                self.brush_colors = brush_colors_palette[c_data]
+
+                if self.attr_size == OWPlotGUI.SizeByOverlap:
+                    # color overlapping points by most frequent color
+                    for i, xy in enumerate(zip(self.x_data, self.y_data)):
+                        if self.overlaps[i] > 1:
+                            cnt = Counter(c_data[j] for j in self.coord_to_id[xy])
+                            c = cnt.most_common(1)[0][0]
+                            self.brush_colors[i] = brush_colors_palette[c]
+                            self.pen_colors[i] = pen_colors_palette[c]
+
             if subset is not None:
                 brush = np.where(
                     subset,

Orange/widgets/visualize/tests/test_owfreeviz.py

@@ -25,14 +25,6 @@ def setUpClass(cls):
     def setUp(self):
         self.widget = self.create_widget(OWFreeViz)
 
-    def test_points_combo_boxes(self):
-        self.send_signal(self.widget.Inputs.data, self.heart_disease)
-        graph = self.widget.controls.graph
-        self.assertEqual(len(graph.attr_color.model()), 17)
-        self.assertEqual(len(graph.attr_shape.model()), 11)
-        self.assertEqual(len(graph.attr_size.model()), 8)
-        self.assertEqual(len(graph.attr_label.model()), 17)
-
     def test_ugly_datasets(self):
         self.send_signal(self.widget.Inputs.data, Table(datasets.path("testing_dataset_cls")))
         self.send_signal(self.widget.Inputs.data, Table(datasets.path("testing_dataset_reg")))

Orange/widgets/visualize/tests/test_owlinearprojection.py

@@ -65,14 +65,6 @@ def test_nan_plot(self):
         with excepthook_catch():
             simulate.combobox_activate_item(cb.attr_size, "X1")
 
-    def test_points_combo_boxes(self):
-        self.send_signal("Data", self.data)
-        graph = self.widget.controls.graph
-        self.assertEqual(len(graph.attr_color.model()), 8)
-        self.assertEqual(len(graph.attr_shape.model()), 3)
-        self.assertEqual(len(graph.attr_size.model()), 6)
-        self.assertEqual(len(graph.attr_label.model()), 8)
-
     def test_buttons(self):
         for btn in self.widget.radio_placement.buttons[:3]:
             self.send_signal(self.widget.Inputs.data, self.data)

Orange/widgets/visualize/tests/test_owradviz.py

@@ -22,14 +22,6 @@ def setUpClass(cls):
     def setUp(self):
         self.widget = self.create_widget(OWRadviz)
 
-    def test_points_combo_boxes(self):
-        self.send_signal(self.widget.Inputs.data, self.heart_disease)
-        graph = self.widget.controls.graph
-        self.assertEqual(len(graph.attr_color.model()), 17)
-        self.assertEqual(len(graph.attr_shape.model()), 11)
-        self.assertEqual(len(graph.attr_size.model()), 8)
-        self.assertEqual(len(graph.attr_label.model()), 17)
-
     def test_ugly_datasets(self):
         self.send_signal(self.widget.Inputs.data, Table(datasets.path("testing_dataset_cls")))
         self.send_signal(self.widget.Inputs.data, Table(datasets.path("testing_dataset_reg")))

Orange/widgets/visualize/tests/test_owscatterplot.py

@@ -8,6 +8,7 @@
 from AnyQt.QtWidgets import QToolTip
 
 from Orange.data import Table, Domain, ContinuousVariable, DiscreteVariable
+from Orange.widgets.utils.plot import OWPlotGUI
 from Orange.widgets.visualize.owscatterplotgraph import MAX
 from Orange.widgets.widget import AttributeList
 from Orange.widgets.tests.base import WidgetTest, WidgetOutputsTestMixin, datasets
@@ -154,15 +155,33 @@ def test_regression_line(self):
     def test_points_combo_boxes(self):
         """Check Point box combo models and values"""
         self.send_signal(self.widget.Inputs.data, self.data)
-        self.assertEqual(len(self.widget.controls.graph.attr_color.model()), 8)
-        self.assertEqual(len(self.widget.controls.graph.attr_shape.model()), 3)
-        self.assertEqual(len(self.widget.controls.graph.attr_size.model()), 6)
-        self.assertEqual(len(self.widget.controls.graph.attr_label.model()), 8)
+        graph = self.widget.controls.graph
+
+        # color and label should contain all variables
+        # size should contain only continuous variables
+        # shape should contain only discrete variables
+        for var in self.data.domain.variables + self.data.domain.metas:
+            self.assertIn(var, graph.attr_color.model())
+            self.assertIn(var, graph.attr_label.model())
+            if var.is_continuous:
+                self.assertIn(var, graph.attr_size.model())
+                self.assertNotIn(var, graph.attr_shape.model())
+            if var.is_discrete:
+                self.assertNotIn(var, graph.attr_size.model())
+                self.assertIn(var, graph.attr_shape.model())
+
         other_widget = self.create_widget(OWScatterPlot)
         self.send_signal(self.widget.Inputs.data, self.data, widget=other_widget)
-        self.assertEqual(self.widget.graph.controls.attr_color.currentText(),
+        self.assertEqual(graph.attr_color.currentText(),
                          self.data.domain.class_var.name)
 
+    def test_overlap(self):
+        self.send_signal(self.widget.Inputs.data, Table("iris"))
+        self.assertEqual(len(set(self.widget.graph.compute_sizes())), 1)
+        simulate.combobox_activate_item(self.widget.controls.graph.attr_size,
+                                        OWPlotGUI.SizeByOverlap)
+        self.assertGreater(len(set(self.widget.graph.compute_sizes())), 1)
+
     def test_group_selections(self):
         self.send_signal(self.widget.Inputs.data, self.data)
         graph = self.widget.graph

doc/visual-programming/source/widgets/visualize/scatterplot.rst

@@ -41,7 +41,8 @@ the left side of the widget. A snapshot below shows the scatterplot of the
 2. Set the color of the displayed points (you will get colors for discrete
    values and grey-scale points for continuous). Set label, shape and
    size to differentiate between points. Set symbol size and opacity for
-   all data points. Set the desired colors scale.
+   all data points. Set the desired colors scale. To visualize the number
+   of overlapping points use *Overlap* for size.
 3. Adjust *plot properties*:
 
    -  *Show legend* displays a legend on the right. Click and drag the legend to move it.