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import pathlib
import unittest
from numpy.testing import assert_allclose
from cogent3 import load_aligned_seqs, make_aligned_seqs, make_table
from cogent3.draw.drawable import AnnotatedDrawable, Drawable, get_domain
from cogent3.util.union_dict import UnionDict
__author__ = "Gavin Huttley"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Gavin Huttley"]
__license__ = "BSD-3"
__version__ = "2023.2.12a1"
__maintainer__ = "Gavin Huttley"
__email__ = "gavin.huttley@anu.edu.au"
__status__ = "Alpha"
def load_alignment(annotate1=False, annotate2=False):
"""creates an alignment with None, one or two sequences annotated"""
path = str(pathlib.Path(__file__).parent.parent / "data/brca1_5.paml")
aln = load_aligned_seqs(path, array_align=False, moltype="dna")
aln = aln.omit_gap_pos()
if annotate1:
aln.get_seq(aln.names[0]).add_feature("gene", "abcde1", [(20, 50)])
aln.get_seq(aln.names[0]).add_feature("variation", "one", [(11, 12)])
if annotate2:
aln.get_seq(aln.names[1]).add_feature("gene", "abcde2", [(20, 50)])
aln.get_seq(aln.names[1]).add_feature("domain", "abcde2", [(10, 15)])
return aln
class UtilDrawablesTests(unittest.TestCase):
"""testing utility functions"""
def test_get_domain_1(self):
"""handles single domain"""
x = get_domain(1, 0, is_y=False)
y = get_domain(1, 0, is_y=True)
assert_allclose(x, [0, 1])
assert_allclose(y, [0, 1])
def test_get_domain_multi(self):
"""produces reversed coordinates for y"""
# plotly coords are cartesian, index coords are array, so they need to
# be converted
y = get_domain(2, 0, is_y=True, space=0)
assert_allclose(y, [0.5, 1])
y = get_domain(2, 1, is_y=True, space=0)
assert_allclose(y, [0, 0.5])
# x-coords unaffected
x = get_domain(2, 0, is_y=False, space=0)
assert_allclose(x, [0, 0.5])
x = get_domain(2, 1, is_y=False, space=0)
assert_allclose(x, [0.5, 1])
def test_get_domain_sep(self):
"""space argument shifts boundaries"""
sep = 0.1
x = get_domain(2, 0, is_y=False, space=sep)
assert_allclose(x, [0 + sep / 2, 0.5 - sep / 2])
x = get_domain(2, 1, is_y=False, space=sep)
assert_allclose(x, [0.5 + sep / 2, 1 - sep / 2])
# if space too big relative to the span of each domain, it's reduced
# to 1/10th the domain span
sep = 0.6
x = get_domain(2, 0, is_y=False, space=sep)
exp_sep = 0.5 / 10
assert_allclose(x, [0 + exp_sep, 0.5 - exp_sep])
def test_domain_element_size(self):
"""domain element value must not exceed num domains - 1"""
with self.assertRaises(ValueError):
x = get_domain(2, 2, is_y=False)
class DrawableObjectTests(unittest.TestCase):
"""testing Drawable object methods and properties"""
def test_traces(self):
"""test trace initialisation"""
d = Drawable()
self.assertEqual(d.traces, [])
trace = dict(type="scatter", x=[0, 1], y=[0, 1])
d = Drawable(traces=[trace])
self.assertEqual(d.traces, [trace])
self.assertTrue(isinstance(d.traces[0], UnionDict))
with self.assertRaises(TypeError):
trace = dict(type="scatter", x=[0, 1], y=[0, 1])
_ = Drawable(traces=trace)
def test_add_traces(self):
"""test trace add method"""
d = Drawable()
self.assertEqual(d.traces, [])
trace = dict(type="scatter", x=[0, 1], y=[0, 1])
d.add_trace(trace)
self.assertEqual(d.traces, [trace])
self.assertTrue(isinstance(d.traces[0], UnionDict))
def test_bound_to(self):
"""bound object should have the drawable object and show methods"""
class TestObj:
pass
o = TestObj()
d = Drawable()
b = d.bound_to(o)
self.assertEqual(b.drawable, d)
self.assertTrue(hasattr(b, "iplot"))
self.assertTrue(hasattr(b, "show"))
def test_figure(self):
"""figure should contain the same data and layout as Drawable"""
trace = dict(type="scatter", x=[0, 1], y=[0, 1])
layout = dict(title="layout", width=20)
d = Drawable(traces=[trace], layout=layout)
f = d.figure
self.assertEqual(f.data, d.traces)
self.assertEqual(f.layout, d.layout)
def test_plotly_figure(self):
"""is a plotly graph object Figure instance"""
from plotly.graph_objects import Figure
trace = dict(type="scatter", x=[0, 1], y=[0, 1])
layout = dict(title="layout", width=20)
d = Drawable(traces=[trace], layout=layout)
self.assertIsInstance(d.plotly_figure, Figure)
class AnnotatedDrawableObjectTests(unittest.TestCase):
"""testing AnnotatedDrawable object methods and properties"""
def test__build_fig(self):
"""figure built should have the same traces as core and set yaxis to y3 if yaxis2 is overlaying"""
trace = dict(type="scatter", x=[0, 1], y=[0, 1], xaxis="x", yaxis="y")
layout = dict(title="layout", width=20, yaxis2=dict(overlaying="free"))
cd = Drawable(traces=[trace])
ad = AnnotatedDrawable(cd, layout=layout)
f = ad._build_fig()
self.assertEqual(ad._traces, f["data"])
self.assertNotEqual(f["data"][0]["yaxis"], "y3")
layout = dict(title="layout", width=20, yaxis2=dict(overlaying="y"))
ad = AnnotatedDrawable(cd, layout=layout)
f = ad._build_fig()
self.assertEqual(f["data"][0]["yaxis"], "y3")
def test_plotly_figure(self):
"""is a plotly graph object Figure instance"""
from plotly.graph_objects import Figure
trace = dict(type="scatter", x=[0, 1], y=[0, 1], xaxis="x", yaxis="y")
layout = dict(title="layout", width=20, yaxis2=dict(overlaying="free"))
cd = Drawable(traces=[trace])
ad = AnnotatedDrawable(cd, layout=layout)
self.assertIsInstance(ad.plotly_figure, Figure)
class BaseDrawablesTests(unittest.TestCase):
"""methods for checking drawables"""
def _check_drawable_attrs(self, fig, type_):
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}, {type_})
def _check_drawable_styles(self, method, styles, **kwargs):
for style in styles:
obj = method(drawable=style, **kwargs)
self._check_drawable_attrs(obj.drawable.figure, style)
class CustomDrawable(BaseDrawablesTests):
"""custom applications of Drawable"""
def test_no_trace(self):
"""should still produce a valid figure"""
d = Drawable()
f = d.figure
self.assertEqual(f.data, [{}])
def test_one_trace(self):
"""should still produce a valid figure"""
d = Drawable()
trace = dict(type="scatter", x=[0, 1], y=[0, 1])
d.add_trace(trace)
f = d.figure
self.assertEqual(f.data, [trace])
def test_layout_with_titles(self):
"""if provided layout has axis titles, keep them"""
layout = dict(xaxis=dict(title="X"), yaxis=dict(title="Y"))
d = Drawable(layout=layout)
fig = d.figure
self.assertEqual(fig.layout.xaxis.title, "X")
self.assertEqual(fig.layout.yaxis.title, "Y")
d = Drawable()
fig = d.figure
self.assertEqual(fig.layout.xaxis.title, None)
self.assertEqual(fig.layout.yaxis.title, None)
def test_layout_with_overrides(self):
"""provided layout attributes should be overridden with provided parameters"""
layout = dict(title="layout", width=20)
d = Drawable(layout=layout)
fig = d.figure
self.assertEqual(fig.layout.title, None)
self.assertEqual(fig.layout.width, None)
d = Drawable(layout=layout, title="parameter", width=50)
fig = d.figure
self.assertEqual(fig.layout.title.text, "parameter")
self.assertEqual(fig.layout.width, 50)
class AlignmentDrawablesTests(BaseDrawablesTests):
"""methods on SequenceCollection produce Drawables"""
def _check_drawable_attrs(self, fig, type_):
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}, {type_})
def _check_drawable_styles(self, method, styles, **kwargs):
for style in styles:
obj = method(drawable=style, **kwargs)
self._check_drawable_attrs(obj.drawable.figure, style)
def test_dotplot_regression(self):
"""Tests whether dotplot produces traces and in correct ordering."""
aln = load_aligned_seqs("data/brca1.fasta", moltype="dna")
aln = aln.take_seqs(["Human", "Chimpanzee"])
aln = aln[:200]
dp = aln.dotplot()
_ = dp.figure
trace_names = [tr.name for tr in dp.traces]
self.assertTrue(
[tr.name for tr in dp.traces] != [] and len(trace_names) == len(dp.traces),
"No traces found for dotplot",
)
self.assertTrue(
[trace_names[i] == dp.traces[i]["name"] for i in range(len(trace_names))],
"Order of traces don't match with dp traces",
)
for trace_name in trace_names:
index = [tr.name for tr in dp.traces].index(trace_name)
dp.traces.pop(index)
self.assertFalse(
trace_name in [tr.name for tr in dp.traces],
"Trace name still present in dp traces even after popping off trace",
)
def test_dotplot_annotated(self):
"""alignment with / without annotated seqs"""
from cogent3.draw.dotplot import Dotplot
aln = load_alignment()
# no annotation
dp = aln.dotplot(name1=aln.names[0], name2=aln.names[1])
self._check_drawable_attrs(dp.figure, "scatter")
self.assertIsInstance(dp, Dotplot)
# seq1 annotated
aln = load_alignment(annotate1=True)
dp = aln.dotplot(name1=aln.names[0], name2=aln.names[1])
self.assertIsInstance(dp, AnnotatedDrawable)
fig = dp.figure
self._check_drawable_attrs(fig, "scatter")
self.assertIs(dp.left_track, None)
self.assertIsInstance(dp.bottom_track, Drawable)
# seq2 annotated
aln = load_alignment(annotate2=True)
dp = aln.dotplot(name1=aln.names[0], name2=aln.names[1])
self.assertIsInstance(dp, AnnotatedDrawable)
fig = dp.figure
self._check_drawable_attrs(fig, "scatter")
self.assertIs(dp.bottom_track, None)
self.assertIsInstance(dp.left_track, Drawable)
# both annotated
aln = load_alignment(True, True)
dp = aln.dotplot(name1=aln.names[0], name2=aln.names[1])
self.assertIsInstance(dp, AnnotatedDrawable)
fig = dp.figure
self._check_drawable_attrs(fig, "scatter")
self.assertIsInstance(dp.bottom_track, Drawable)
self.assertIsInstance(dp.left_track, Drawable)
def test_annotated_dotplot_remove_tracks(self):
"""removing annotation tracks from dotplot should work"""
# both annotated
aln = load_alignment(True, True)
dp = aln.dotplot(name1=aln.names[0], name2=aln.names[1])
orig_fig = dp.figure
# remove left
dp.remove_track(left_track=True)
self.assertIs(dp.left_track, None)
self.assertEqual(dp._traces, [])
self.assertIsNot(dp.figure, orig_fig)
self.assertIsInstance(dp.figure, UnionDict)
# both annotated, remove right
dp = aln.dotplot(name1=aln.names[0], name2=aln.names[1])
dp.remove_track(bottom_track=True)
self.assertIs(dp.bottom_track, None)
self.assertEqual(dp._traces, [])
self.assertIsNot(dp.figure, orig_fig)
self.assertIsInstance(dp.figure, UnionDict)
# both annotated, remove both
dp = aln.dotplot(name1=aln.names[0], name2=aln.names[1])
dp.remove_track(True, True)
self.assertIs(dp.bottom_track, None)
self.assertIs(dp.left_track, None)
self.assertEqual(dp._traces, [])
self.assertIsNot(dp.figure, orig_fig)
self.assertIsInstance(dp.figure, UnionDict)
def test_count_gaps_per_seq(self):
"""creation of drawables works"""
styles = "bar", "box", "violin"
aln = load_alignment(False, False)
# no drawable
counts = aln.count_gaps_per_seq()
self.assertFalse(hasattr(counts, "drawable"))
self._check_drawable_styles(aln.count_gaps_per_seq, styles)
# now ArrayAlignment
aln = aln.to_type(array_align=True)
self._check_drawable_styles(aln.count_gaps_per_seq, styles)
def test_coevo_drawables(self):
"""coevolution produces drawables"""
styles = "box", "heatmap", "violin"
aln = load_alignment(False, False)
aln = aln[:10]
coevo = aln.coevolution(show_progress=False)
self.assertFalse(hasattr(coevo, "drawable"))
self._check_drawable_styles(aln.coevolution, styles, show_progress=False)
# now ArrayAlignment
aln = aln.to_type(array_align=True)
self._check_drawable_styles(aln.coevolution, styles, show_progress=False)
def test_coevo_annotated(self):
"""coevolution on alignment with annotated seqs should add to heatmap plot"""
aln = load_alignment(True, False)
aln = aln[30:]
coevo = aln.coevolution(show_progress=False, drawable="heatmap")
drawable = coevo.drawable
self.assertIsInstance(drawable, AnnotatedDrawable)
self.assertIsInstance(drawable.left_track, Drawable)
self.assertIsInstance(drawable.bottom_track, Drawable)
def test_information_plot(self):
"""infoprmation plot makes a drawable"""
aln = load_alignment(False, False)
drawable = aln.information_plot()
self.assertIsInstance(drawable, Drawable)
self._check_drawable_attrs(drawable.figure, "scatter")
# ArrayAlignment
aln = aln.to_type(array_align=True)
drawable = aln.information_plot()
self._check_drawable_attrs(drawable.figure, "scatter")
def test_get_drawable(self):
"""sliced alignment with features returns a drawable"""
aln = make_aligned_seqs(
data=dict(a="AAACGGTTT", b="CAA--GTAA"), array_align=False
)
_ = aln.get_seq("b").add_feature("domain", "1", [(1, 5)])
_ = aln.get_seq("b").add_feature("variation", "1", [(1, 5)])
_ = aln.get_seq("b").add_feature("gene", "1", [(1, 5)])
_ = aln.get_seq("b").add_feature("gene", "1", [(5, 1)])
aln.get_drawable()
class TableDrawablesTest(BaseDrawablesTests):
"""single Table method produces a Drawable"""
def test_to_plotly(self):
"""exercise producing a plotly table"""
table = make_table(header=["a", "b"], data=[[0, 1]], index_name="a")
drawable = table.to_plotly()
self.assertIsInstance(drawable, Drawable)
self._check_drawable_attrs(drawable.figure, "table")
if __name__ == "__main__":
unittest.main()
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