Default subplots to time difference from first sample

But also allow calendar date, if required.

This makes it much easier to compare plots from ARGs with different endpoints

sc2ts/info.py

@@ -1617,6 +1617,9 @@ def draw_subtree(
         extra_tracked_samples=None,
         pack_untracked_polytomies=True,
         time_scale="rank",
+        y_ticks=None,
+        y_label=None,
+        date_format=None,
         title=None,
         mutation_labels=None,
         append_mutation_recurrence=None,
@@ -1647,6 +1650,12 @@ def draw_subtree(
             containing tracked nodes. If ``None`` (default), do not collapse
             any such clades , otherwise only collapse them when they contain more
             than a fraction `collapse_tracked` of tracked nodes.
+        :param date_format str: How to format the displayed node date: one of "ts" (use
+            the tree sequence time, usually where the most recent sample is at zero),
+            "from_zero" (set the earliest sample to zero and count time as negative
+            days from the start of the genealogy), or "cal" (use the calendar date from
+            the sample metadata, hence do not display times for nonsample nodes).
+            Default: ``None`` treated as "from_zero".
         :param remove_clones bool: Whether to remove samples that are clones of other
             samples (i.e. that have no mutations above them). Currently unimplemented.
         :param extra_tracked_samples list: Additional nodes to track in the tree, to
@@ -1658,11 +1667,14 @@ def draw_subtree(
         :param mutation_labels dict: A dictionary mapping mutation IDs to labels. If not
             provided, mutation labels are generated automatically, in the form
             ``{inherited_state}{position}{derived_state}``
-        :params append_mutation_dupes bool: If True (default), append a count to the
+        :param append_mutation_dupes bool: If True (default), append a count to the
             mutation label indicating the number of other such mutations above the
             shown nodes that are at the same position and to the same derived state.
         :param time_scale str: As for the ``time_scale`` parameter of `draw_svg()`, but
             defaults to "rank".
+        :param y_label str: As for the ``y_label`` parameter of `draw_svg()`.
+        :param y_ticks array: As for the ``y_ticks`` parameter of `draw_svg()`. Cannot be
+            combined with ``date_format="cal"``.
 
         .. note::
             By default, styles are set such that tracked pango / strain / sample nodes
@@ -1676,6 +1688,15 @@ def draw_subtree(
             position = 21563  # pick the start of the spike
         if size is None:
             size = (1000, 1000)
+        if date_format is None:
+            date_format = "from_zero"
+        if y_label is None:
+            if date_format == "cal":
+                y_label = "Calendar date"
+            elif date_format == "ts":
+                y_label = f"Time ({self.ts.time_units} ago)"
+            else:
+                y_label = f"Time difference from earliest sample ({self.ts.time_units})"
         if append_mutation_recurrence is None:
             append_mutation_recurrence = True
         if remove_clones:
@@ -1686,7 +1707,14 @@ def draw_subtree(
         time = tables.mutations.time
         time[:] = tskit.UNKNOWN_TIME
         tables.mutations.time = time
+        #rescale to negative times
+        if date_format == "from_zero":
+            for node in reversed(self.ts.nodes(order="timeasc")):
+                if node.is_sample():
+                    break
+            tables.nodes.time = tables.nodes.time - node.time
         ts = tables.tree_sequence()
+
 
         tracked_nodes = []
         if tracked_pango is not None:
@@ -1725,7 +1753,7 @@ def draw_subtree(
 
         if title is None:
             title = f"Sc2ts genealogy of {len(tracked_nodes)} samples. "
-        simplified_ts = self.ts.simplify(
+        simplified_ts = ts.simplify(
             order[np.where(ts.nodes_flags[order] & tskit.NODE_IS_SAMPLE)[0]]
         )
         num_trees = simplified_ts.num_trees
@@ -1822,15 +1850,32 @@ def draw_subtree(
             ",".join([f".node.n{u} > .sym" for u in re_nodes])
             + f"{{r:{symbol_size/2*1.5:.2f}px; stroke:black; fill:white}}"
         )
+        if date_format == "cal":
+            if y_ticks is not None:
+                raise ValueError("Cannot set y_ticks when date_format='cal'")
+            shown_times = ts.nodes_time[shown_nodes]
+            if time_scale == "rank":
+                _, index = np.unique(shown_times, return_index=True)
+                y_ticks = {
+                    i: ts.node(shown_nodes[t]).metadata.get("date", "")
+                    for i, t in enumerate(index)
+                }
+            else:
+                # only place ticks at the sample nodes
+                y_ticks = {t: ts.node(u).metadata.get("date", "")
+                           for u, t in zip(shown_nodes, shown_times)
+                }
         return tree.draw_svg(
             time_scale=time_scale,
             y_axis=True,
             x_axis=False,
+            y_label=y_label,
             title=title,
             size=size,
             order=order,
             mutation_labels=mut_labels,
             all_edge_mutations=True,
+            y_ticks=y_ticks,
             symbol_size=symbol_size,
             pack_untracked_polytomies=pack_untracked_polytomies,
             style="".join(styles) + style,