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)