naively handling case for heatmap where time units are uncalibrated.

Author: savitakartik

model.py

@@ -595,43 +595,57 @@ def compute_ancestor_spans_heatmap_data(self, num_x_bins, num_y_bins):
         """
         Calculates the average ancestor span in a genomic-time window
         """
-        nodes_df = self.nodes_df[self.nodes_df.ancestors_span != -np.inf]
-        nodes_df = nodes_df.reset_index(drop=True)
-        nodes_left = nodes_df.child_left
-        nodes_right = nodes_df.child_right
-        nodes_time = nodes_df.time
-
-        x_bins = np.linspace(nodes_left.min(), nodes_right.max(), num_x_bins + 1)
-        y_bins = np.linspace(0, nodes_time.max(), num_y_bins + 1)
-        heatmap_counts = np.zeros((num_x_bins, num_y_bins))
-
-        x_starts = np.digitize(nodes_left, x_bins, right=True)
-        x_ends = np.digitize(nodes_right, x_bins, right=True)
-        y_starts = np.digitize(nodes_time, y_bins, right=True)
-
-        for u in range(len(nodes_left)):
-            x_start = max(0, x_starts[u] - 1)
-            x_end = max(0, x_ends[u] - 1)
-            y_bin = max(0, y_starts[u] - 1)
-            heatmap_counts[x_start : x_end + 1, y_bin] += 1
-
-        x_coords = np.repeat(x_bins[:-1], num_y_bins)
-        y_coords = np.tile(y_bins[:-1], num_x_bins)
-        overlapping_node_count = heatmap_counts.flatten()
-        overlapping_node_count[overlapping_node_count == 0] = 1
-        # FIXME - better way to avoid log 0 above?
-        df = pd.DataFrame(
-            {
-                "position": x_coords.flatten(),
-                "time": y_coords.flatten(),
-                "overlapping_node_count_log10": np.log10(overlapping_node_count),
-                "overlapping_node_count": overlapping_node_count,
-            }
-        )
-        return df.astype(
-            {
-                "position": "int",
-                "time": "int",
-                "overlapping_node_count": "int",
-            }
-        )
+        if self.ts.time_units == tskit.TIME_UNITS_UNCALIBRATED:
+            logger.warning(
+                "Cannot compute ancestor spans for uncalibrated tree sequence"
+            )
+            return pd.DataFrame(
+                {
+                    "position": [],
+                    "time": [],
+                    "overlapping_node_count_log10": [],
+                    "overlapping_node_count": [],
+                }
+            )
+        else:
+            nodes_df = self.nodes_df[self.nodes_df.ancestors_span != -np.inf]
+            nodes_df = nodes_df.reset_index(drop=True)
+            nodes_left = nodes_df.child_left
+            nodes_right = nodes_df.child_right
+            nodes_time = nodes_df.time
+
+            x_bins = np.linspace(nodes_left.min(), nodes_right.max(), num_x_bins + 1)
+            y_bins = np.linspace(0, nodes_time.max(), num_y_bins + 1)
+            heatmap_counts = np.zeros((num_x_bins, num_y_bins))
+
+            x_starts = np.digitize(nodes_left, x_bins, right=True)
+            x_ends = np.digitize(nodes_right, x_bins, right=True)
+            y_starts = np.digitize(nodes_time, y_bins, right=True)
+
+            for u in range(len(nodes_left)):
+                x_start = max(0, x_starts[u] - 1)
+                x_end = max(0, x_ends[u] - 1)
+                y_bin = max(0, y_starts[u] - 1)
+                heatmap_counts[x_start : x_end + 1, y_bin] += 1
+
+            x_coords = np.repeat(x_bins[:-1], num_y_bins)
+            y_coords = np.tile(y_bins[:-1], num_x_bins)
+            overlapping_node_count = heatmap_counts.flatten()
+            overlapping_node_count[overlapping_node_count == 0] = 1
+            # FIXME - better way to avoid log 0 above?
+            df = pd.DataFrame(
+                {
+                    "position": x_coords.flatten(),
+                    "time": y_coords.flatten(),
+                    "overlapping_node_count_log10": np.log10(overlapping_node_count),
+                    "overlapping_node_count": overlapping_node_count,
+                }
+            )
+            return df.astype(
+                {
+                    "position": "int",
+                    "time": "int",
+                    "overlapping_node_count_log10": "int",
+                    "overlapping_node_count": "int",
+                }
+            )

pages/nodes.py

@@ -103,6 +103,7 @@ def make_heatmap(num_x_bins, num_y_bins):
     )
 
     return pn.Column(
-        pn.Row(main, pn.Column(hist_panel, plot_options)),
+        pn.Column(main),
+        pn.Column(hist_panel, plot_options),
         pn.Column(hm_panel, hm_options),
     )