def test_dendro_with_support(self):
"""exercising creating dendrograms with support measure"""
data = {
"newick": "(A,(B,C)edge.1,(D,E)edge.0)",
"edge_attributes": {
"A": {"support": 1.0, "length": 0.148},
"B": {"support": 1.0, "length": 0.098},
"C": {"support": 1.0, "length": 0.134},
"edge.1": {"support": 0.8, "length": 0.016},
"D": {"support": 1.0, "length": 0.087},
"E": {"support": 1.0, "length": 0.048},
"edge.0": {"support": 0.6, "length": 0.131},
"root": {"length": None},
},
"type": "cogent3.core.tree.PhyloNode",
"version": "2019.10.17a",
}
tree = deserialise_object(data)
# currently not supported for "circular", "radial"
for style in ("square", "angular"):
y_support = Dendrogram(tree, style=style, show_support=True, threshold=0.8)
n_support = Dendrogram(tree, style=style, show_support=False)
self.assertEqual(
len(y_support.figure.layout.annotations)
- len(n_support.figure.layout.annotations),
2,
style,
)
def test_tip_font(self):
"""test tip_font settable"""
tree = make_tree(treestring="(a,b,(c,(d,e)e1)e2)")
dnd = Dendrogram(tree=tree)
dnd.tip_font |= dict(size=18)
self.assertEqual(dnd.tip_font.size, 18)
dnd.tip_font.size = 10
self.assertEqual(dnd.tip_font.size, 10)
dnd.tip_font.color = "red"
self.assertEqual(dnd.tip_font["color"], "red")
def test_style_edges(self):
"""test style_edges only accepts edges present in tree"""
tree = make_tree(treestring="(a,b,(c,(d,e)e1)e2)")
dnd = Dendrogram(tree=tree)
dnd.style_edges("a", line=dict(color="magenta"))
with self.assertRaises(ValueError):
dnd.style_edges("foo", line=dict(color="magenta"))
def test_dendro_shape(self):
"""exercising using different values of shape parameter"""
tree = make_tree(treestring="(a:0.1,b:0.1,(c:0.05,(d:0.01,e:0.02):0.01):0.1)")
for style in ("square", "angular", "circular", "radial"):
dnd = Dendrogram(tree, style=style)
# the figure attribute should be a dict
fig = dnd.figure
self.assertIsInstance(fig, UnionDict)
# should have a layout and a data key
self.assertTrue("layout" in fig)
self.assertTrue("data" in fig)
# data traces should be of type "scatter"
self.assertEqual({tr.type for tr in fig.data}, {"scatter"})
def test_square_dendrogram_regression(self):
tree = make_tree(treestring="(a:0.1,b:0.1,(c:0.05,(d:0.01,e:0.02):0.01):0.1)")
dendrogram = Dendrogram(tree, style="square", contemporaneous=False)
func = dendrogram.tree.get_node_matching_name
actual_vals = [
(func("root").x, func("root").y),
(func("a").x, func("a").y),
(func("b").x, func("b").y),
(func("c").x, func("c").y),
(func("d").x, func("d").y),
(func("e").x, func("e").y),
]
expected_vals = [
(0, 1.3),
(0.1, 2.6),
(0.1, 1.3),
(0.15, -2.6),
(0.12, 0),
(0.13, -1.3),
]
assert_allclose(actual_vals, expected_vals)
def test_get_edges(self):
"""returns edge names"""
tree = make_tree(treestring="(a,b,(c,(d,e)e1)e2)")
dnd = Dendrogram(tree=tree)
edges = dnd.get_edge_names("d", "c", clade=True, stem=False)
self.assertEqual(set(edges), set(["c", "d", "e", "e1"]))