def draw(self):
hierarchy = self.hierarchy.rescale()
self_data = np.array([(c.res1, c.res1_seq, c.res2, c.res2_seq,
c.raw_score, c.status) for c in hierarchy])
_drange = np.append(self_data[:, 1], self_data[:, 3]).astype(np.int64)
self_data_range = np.arange(_drange.min(), _drange.max() + 1)
npoints = self_data_range.shape[0]
coords = np.array(get_points_on_circle(npoints))
bezier_path = np.arange(0, 1.01, 0.01)
for c in self_data:
x1, y1 = coords[int(c[1]) - self_data_range.min()]
x2, y2 = coords[int(c[3]) - self_data_range.min()]
xb, yb = [0, 0]
x = (1 - bezier_path)**2 * x1 + 2 * (
1 - bezier_path) * bezier_path * xb + bezier_path**2 * x2
y = (1 - bezier_path)**2 * y1 + 2 * (
1 - bezier_path) * bezier_path * yb + bezier_path**2 * y2
alpha = float(c[4]) if self.use_conf else 1.0
color = {
ContactMatchState.false_positive: ColorDefinitions.MISMATCH,
ContactMatchState.true_positive: ColorDefinitions.MATCH,
}.get(int(c[5]), ColorDefinitions.MATCH)
self.ax.plot(x,
y,
color=color,
alpha=alpha,
linestyle="-",
zorder=0)
if int(c[5]) == ContactMatchState.true_positive:
self.ax.plot(x,
y,
color=color,
alpha=alpha,
linestyle="-",
zorder=1,
linewidth=1)
else:
self.ax.plot(x,
y,
color=color,
alpha=alpha,
linestyle="-",
zorder=0,
linewidth=1)
residue_data = np.append(self_data[:, [1, 0]], self_data[:, [3, 2]])
residue_data = residue_data.reshape(self_data[:, 0].shape[0] * 2, 2)
color_codes = dict([(k, ColorDefinitions.AA_ENCODING["X"])
for k in self_data_range])
for k, v in np.vstack([tuple(row) for row in residue_data]):
color_codes[int(k)] = ColorDefinitions.AA_ENCODING[v]
colors = [color_codes[k] for k in sorted(color_codes.keys())]
# TODO: Use tools module to process this
x, _ = zip(*residue_data)
label_data = set(map(int, x))
label_coords = np.zeros((npoints, 2))
space = 2 * np.pi / npoints
for i in np.arange(npoints):
label_coords[i] = [
(npoints + npoints / 10) * np.cos(space * i) - npoints / 20,
(npoints + npoints / 10) * np.sin(space * i) - npoints / 40,
]
xy_highlight = []
for r in sorted(label_data)[::int(npoints / (npoints / 10))]:
i = r - self_data_range.min()
xy = coords[i]
xytext = label_coords[i]
self.ax.annotate(r, xy=xy, xytext=xytext)
xy_highlight.append(xy.tolist())
radius = get_radius_around_circle(coords[0], coords[1])
self._patch_scatter(coords[:, 0],
coords[:, 1],
symbol="o",
facecolor=colors,
linewidth=0.0,
radius=radius)
self._patch_scatter(*zip(*xy_highlight),
symbol="o",
facecolor="none",
edgecolor="#000000",
radius=radius)
arrow_x, arrow_y = (npoints + npoints / 5, 0)
self.ax.arrow(arrow_x,
arrow_y,
0,
npoints / 10,
head_width=1.5,
color="#000000")
self.ax.set_xlim(-arrow_x, arrow_x + 2)
self.ax.set_ylim(-arrow_x, arrow_x)
self.ax.axis("off")
# TODO: deprecate this in 0.14
if self._file_name:
self.savefig(self._file_name, dpi=self._dpi)
def test_get_points_on_circle_6(self):
coords = tools.get_points_on_circle(4, h=2)
self.assertEqual([6.0, 0.0], coords[0])
self.assertEqual([2.0, 4.0], coords[1])
self.assertEqual([-2.0, 0.0], coords[2])
self.assertEqual([2, -4], coords[3])
def test_get_points_on_circle_7(self):
coords = tools.get_points_on_circle(4, k=-3)
self.assertEqual([4.0, -3.0], coords[0])
self.assertEqual([0.0, 1.0], coords[1])
self.assertEqual([-4.0, -3.0], coords[2])
self.assertEqual([0, -7], coords[3])
def test_get_points_on_circle_5(self):
coords = tools.get_points_on_circle(4)
self.assertEqual([4.0, 0.0], coords[0])
self.assertEqual([0.0, 4.0], coords[1])
self.assertEqual([-4.0, 0.0], coords[2])
self.assertEqual([0, -4], coords[3])
def test_get_points_on_circle_4(self):
coords = tools.get_points_on_circle(3)
self.assertEqual([3.0, 0.0], coords[0])
self.assertEqual([-1.5, 2.598076], coords[1])
self.assertEqual([-1.5, -2.598076], coords[2])
def test_get_points_on_circle_3(self):
coords = tools.get_points_on_circle(2)
self.assertEqual([2.0, 0.0], coords[0])
self.assertEqual([-2.0, 0], coords[1])
def test_get_points_on_circle_2(self):
coords = tools.get_points_on_circle(1)
self.assertEqual([[1.0, 0.0]], coords)
def test_get_points_on_circle_1(self):
coords = tools.get_points_on_circle(0)
self.assertEqual([[]], coords)
