Merge pull request #96 from natetrux/9_9fixes

Annotate subpackage fixes
eaton-lab · Sep 13, 2024 · 0b2ee6a · 0b2ee6a
2 parents f9eb409 + dc6f314
commit 0b2ee6a
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Showing 3 changed files with 6 additions and 5 deletions.
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -116,7 +116,7 @@ nav:
       - quadripartition methods: quadripartitions.ipynb
       # - other: ...
 
-    - <i>.distance</i> - tree/node dists: # TO DO
+    - <i>.distance</i> - tree/node dists: 
       - node distances: node-distance.ipynb
       - tree distances: tree-distance.ipynb
 

diff --git a/toytree/annotate/__init__.py b/toytree/annotate/__init__.py
@@ -49,6 +49,7 @@
 from toytree.annotate.src.add_tip_markers import *
 from toytree.annotate.src.add_axes_box_outline import *
 from toytree.annotate.src.add_scale_bar import *
+from toytree.annotate.src.add_pie_markers import *
 
 # ... edge_labels
 # ... node_labels

diff --git a/toytree/annotate/src/add_pie_markers.py b/toytree/annotate/src/add_pie_markers.py
@@ -12,7 +12,7 @@
 from toytree.style import check_arr, get_color_mapped_values
 from toytree.annotate.src.checks import get_last_toytree_mark, assert_tree_matches_mark
 from toytree.core.apis import add_subpackage_method, AnnotationAPI
-from toytree.annotate.src.add_edge_markers import _get_edge_midpoints
+from toytree.annotate.src.add_edge_markers import get_edge_midpoints
 from toytree.drawing.src.mark_pie import PieChartMark
 from toytree.style.src.validate_data import (
     validate_numeric,
@@ -248,7 +248,8 @@ def add_edge_pie_charts(
 
     # get coordinates of all real edges
     nedges = tree.nnodes - 2 if tree.is_rooted() else tree.nnodes - 1
-    coords = _get_edge_midpoints(tree, mark.ntable, mark.layout, mark.edge_type)
+    #coords = _get_edge_midpoints(tree, mark.ntable, mark.layout, mark.edge_type)
+    coords = get_edge_midpoints(mark.etable, mark.ntable, mark.layout, mark.edge_type)
 
     mask = validate_mask(tree, style={"node_mask": mask})[:nedges]
 
@@ -302,15 +303,14 @@ def add_edge_pie_charts(
     import toytree
     tree = toytree.rtree.unittree(6, seed=123)
     canvas, axes, m0 = tree.draw()
-
     # generate random pie-like (proportion) data array
     import numpy as np
     ncategories = 3
     arr = np.random.random(size=(tree.nnodes, ncategories))
     arr = (arr.T / arr.sum(axis=1)).T
 
     # add pie charts to all internal Nodes
-    tree.annotate.add_edge_pie_charts(
+    tree.annotate.add_node_pie_charts(
         axes=axes,
         data=arr,
         size=20,