diff --git a/mkdocs.yml b/mkdocs.yml index 8586c738..e89a2179 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -116,7 +116,7 @@ nav: - quadripartition methods: quadripartitions.ipynb # - other: ... - - .distance - tree/node dists: # TO DO + - .distance - 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 index e0a6edbe..c8c6883e 100644 --- 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 index 2cde49c1..7a3adc69 100644 --- 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] @@ -302,7 +303,6 @@ 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 @@ -310,7 +310,7 @@ def add_edge_pie_charts( 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,