fix 0.PE subclades and add blank label

ktmeaton · May 4, 2021 · 6b03980 · 6b03980
1 parent 51a9883
commit 6b03980
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Showing 3 changed files with 671 additions and 580 deletions.
diff --git a/workflow/notebooks/auspice.py.ipynb b/workflow/notebooks/auspice.py.ipynb
diff --git a/workflow/notebooks/functions.py b/workflow/notebooks/functions.py
@@ -352,7 +352,7 @@ def auspice_export(
 
 def branch_attributes(tree_dict, sub_dict, df, label_col):
     """
-    Add branch attributes to an auspice tree
+    Add branch attributes to an auspice tree.
     """
     root = sub_dict
     if "children" not in root:
@@ -371,6 +371,9 @@ def branch_attributes(tree_dict, sub_dict, df, label_col):
                     .replace("_", " ")
                     .title()
                 )
+                # clade needs to stay lowercase
+                if col == "clade":
+                    col_pretty = "clade"
                 branch_labels[col_pretty] = df[col][node["name"]]
 
             node["branch_attrs"]["labels"] = branch_labels
@@ -383,6 +386,9 @@ def branch_attributes(tree_dict, sub_dict, df, label_col):
                 .replace("_", " ")
                 .title()
             )
+            # clade needs to stay lowercase
+            if col == "clade":
+                col_pretty = "clade"
             branch_labels[col_pretty] = df[col][node["name"]]
         root["branch_attrs"]["labels"] = branch_labels
         return root

diff --git a/workflow/notebooks/iqtree_stats.py.ipynb b/workflow/notebooks/iqtree_stats.py.ipynb