Merge pull request #398 from hyanwong/mut-plotting

Make mutation labelling more flexible

sc2ts/info.py

@@ -1619,6 +1619,7 @@ def draw_subtree(
         time_scale="rank",
         title=None,
         mutation_labels=None,
+        append_mutation_recurrence=None,
         size=None,
         style="",
         symbol_size=4,
@@ -1656,8 +1657,10 @@ def draw_subtree(
             be placed on the right, and condensed into a dotted line? Default: ``True``
         :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}``, with counts added if there
-            are recurrent mutations.
+            ``{inherited_state}{position}{derived_state}``
+        :params 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".
 
@@ -1673,6 +1676,8 @@ def draw_subtree(
             position = 21563  # pick the start of the spike
         if size is None:
             size = (1000, 1000)
+        if append_mutation_recurrence is None:
+            append_mutation_recurrence = True
         if remove_clones:
             # TODO
             raise NotImplementedError("remove_clones not implemented")
@@ -1751,38 +1756,43 @@ def draw_subtree(
                     shown_nodes.append(u)
                 prev = u
 
-        if mutation_labels is None:
-            mutation_labels = collections.defaultdict(list)
-            multiple_mutations = []
-            reverted_mutations = []
-            use_mutations = np.where(np.isin(ts.mutations_node, shown_nodes))[0]
-            sites = ts.mutations_site[use_mutations]
-            for mut_id in use_mutations:
-                # TODO Viz the recurrent mutations
-                mut = ts.mutation(mut_id)
-                site = ts.site(mut.site)
-                if np.sum(sites == site.id) > 1:
-                    multiple_mutations.append(mut.id)
-                inherited_state = site.ancestral_state
-                if mut.parent >= 0:
-                    parent = ts.mutation(mut.parent)
-                    inherited_state = parent.derived_state
-                    parent_inherited_state = site.ancestral_state
-                    if parent.parent >= 0:
-                        parent_inherited_state = ts.mutation(
-                            parent.parent
-                        ).derived_state
-                    if parent_inherited_state == mut.derived_state:
-                        reverted_mutations.append(mut.id)
-                # Reverse map label name to mutation id, so we can count duplicates
-                label = f"{inherited_state}{int(site.position)}{mut.derived_state}"
-                mutation_labels[label].append(mut.id)
+        multiple_mutations = []
+        reverted_mutations = []
+        recurrent_mutations = collections.defaultdict(list)
+        mut_labels = {} if mutation_labels is None else mutation_labels.copy()
+        use_mutations = np.where(np.isin(ts.mutations_node, shown_nodes))[0]
+        sites = ts.mutations_site[use_mutations]
+        for mut_id in use_mutations:
+            # TODO Viz the recurrent mutations
+            mut = ts.mutation(mut_id)
+            site = ts.site(mut.site)
+            if np.sum(sites == site.id) > 1:
+                multiple_mutations.append(mut.id)
+            inherited_state = site.ancestral_state
+            if mut.parent >= 0:
+                parent = ts.mutation(mut.parent)
+                inherited_state = parent.derived_state
+                parent_inherited_state = site.ancestral_state
+                if parent.parent >= 0:
+                    parent_inherited_state = ts.mutation(
+                        parent.parent
+                    ).derived_state
+                if parent_inherited_state == mut.derived_state:
+                    reverted_mutations.append(mut.id)
+            pos = int(site.position)
+            recurrent_mutations[(pos, mut.derived_state)].append(mut.id)
+            if mutation_labels is None:
+                mut_labels[mut.id] = f"{inherited_state}{pos}{mut.derived_state}"
             # If more than one mutation has the same label, add a prefix with the counts
-            mutation_labels = {
-                m_id: label + (f" ({i+1}/{len(ids)})" if len(ids) > 1 else "")
-                for label, ids in mutation_labels.items()
-                for i, m_id in enumerate(ids)
+        if append_mutation_recurrence:
+            num_recurrent = {
+                m_id: (i+1, len(ids))
+                for ids in recurrent_mutations.values() for i, m_id in enumerate(ids)
+                if len(ids) > 1
             }
+            for m_id, (i, n) in num_recurrent.items():
+                if m_id in mut_labels:
+                    mut_labels[m_id] += f" ({i}/{n})"
         # some default styles
         styles = [
             "".join(f".n{u} > .sym {{fill: cyan}}" for u in tracked_nodes),
@@ -1819,7 +1829,7 @@ def draw_subtree(
             title=title,
             size=size,
             order=order,
-            mutation_labels=mutation_labels,
+            mutation_labels=mut_labels,
             all_edge_mutations=True,
             symbol_size=symbol_size,
             pack_untracked_polytomies=pack_untracked_polytomies,

sc2ts/utils.py

@@ -355,7 +355,7 @@ def sort_mutation_label(s):
                 s = (
                     s.replace("$", "")
                     .replace(r"\bf", "")
-                    .replace("\it", "")
+                    .replace(r"\it", "")
                     .replace("{", "")
                     .replace("}", "")
                 )