def draw_peak_pair(self, pair, color='red', alpha=0.8, fontsize=12, label=None, rotation=45, **kwargs): p1, p2 = pair self.ax.plot((p1.mz, p2.mz), (p1.intensity, p2.intensity), color=color, alpha=alpha, **kwargs) draw_peaklist(pair, ax=self.ax, alpha=0.4, color='orange') if label: midx = (p1.mz + p2.mz) / 2 # interpolate the midpoint's height midy = (p1.intensity * (p2.mz - midx) + p2.intensity * (midx - p1.mz)) / (p2.mz - p1.mz) if isinstance(label, (list, tuple)): label = '-'.join(map(str, label)) else: label = str(label) self.ax.text(midx, midy, label, fontsize=fontsize, ha='center', va='bottom', rotation=rotation, clip_on=True)
def draw_peak_pair(self, pair, color='red', alpha=0.8, fontsize=12, label=None, rotation=45, **kwargs): p1, p2 = pair self.ax.plot((p1.mz, p2.mz), (p1.intensity, p2.intensity), color=color, alpha=alpha, **kwargs) kwargs.setdefault("clip_on", self.clip_labels) clip_on = kwargs['clip_on'] draw_peaklist(pair, ax=self.ax, alpha=0.4, color='orange') if label: midx = (p1.mz + p2.mz) / 2 # interpolate the midpoint's height midy = (p1.intensity * (p2.mz - midx) + p2.intensity * (midx - p1.mz)) / (p2.mz - p1.mz) # find the angle of the line connecting the two peaks xlo = min(p1.mz, p2.mz) xhi = max(p1.mz, p2.mz) adj = xhi - xlo ylo = min(p1.intensity, p2.intensity) yhi = max(p1.intensity, p2.intensity) opp = yhi - ylo hypot = np.hypot(adj, opp) rotation = np.arccos(adj / hypot) if isinstance(label, (list, tuple)): label = '-'.join(map(str, label)) else: label = str(label) self.ax.text(midx, midy, label, fontsize=fontsize, ha='center', va='bottom', rotation=rotation, clip_on=clip_on)
def _ghost_in_theoretical_envelopes(self): ax = self.ax for result in self.results: draw_peaklist(result.fit.theoretical, ax=ax, color='green', alpha=0.5, lw=0.5)
def draw_all_peaks(self, color='black', alpha=0.5, **kwargs): draw_peaklist( self.spectrum_match.deconvoluted_peak_set, alpha=0.3, color='grey', ax=self.ax, **kwargs) try: draw_peaklist( self.spectrum_match._sanitized_spectrum, color='grey', ax=self.ax, alpha=0.5, **kwargs) except AttributeError: pass
def _highlight_matched_envelopes(self): ax = self.ax for result in self.results: score = result['score'] a = max(1 - score, 0.1) draw_peaklist(result.fit.experimental, ax=ax, color='red', alpha=a, lw=0.5)
def draw_matched_peaks(self, color='red', alpha=0.8, fontsize=12, ion_series_to_color=None, **kwargs): if ion_series_to_color is None: ion_series_to_color = {} try: solution_map = self.spectrum_match.solution_map except AttributeError: return for peak, fragment in solution_map: try: peak_color = ion_series_to_color.get(fragment.series, color) except AttributeError: peak_color = ion_series_to_color.get(fragment.kind, color) draw_peaklist([peak], alpha=alpha, ax=self.ax, color=peak_color) self.label_peak(fragment, peak, fontsize=fontsize, **kwargs)
def draw_all_peaks(self, color='black', alpha=0.5, **kwargs): draw_peaklist(self.spectrum_match.spectrum, alpha=0.3, color='grey', ax=self.ax, **kwargs) try: draw_peaklist(self.spectrum_match._sanitized_spectrum, color='grey', ax=self.ax, alpha=0.5, **kwargs) except AttributeError: pass
def draw_matched_peaks(self, color='red', alpha=0.8, fontsize=12, ion_series_to_color=None, **kwargs): if ion_series_to_color is None: ion_series_to_color = {} for peak, fragment in self.spectrum_match.solution_map: try: peak_color = ion_series_to_color.get(fragment.series, color) except AttributeError: peak_color = ion_series_to_color.get(fragment.kind, color) draw_peaklist([peak], alpha=alpha, ax=self.ax, color=peak_color) self.label_peak(fragment, peak, fontsize=fontsize, **kwargs)
def draw_peak_pair(self, pair, color='red', alpha=0.8, fontsize=12, label=None, rotation=45, **kwargs): p1, p2 = pair self.ax.plot((p1.mz, p2.mz), (p1.intensity, p2.intensity), color=color, alpha=alpha, **kwargs) kwargs.setdefault("clip_on", self.clip_labels) clip_on = kwargs['clip_on'] draw_peaklist(pair, ax=self.ax, alpha=0.4, color='orange') if label: # pylint: disable=assignment-from-no-return midx = (p1.mz + p2.mz) / 2 # interpolate the midpoint's height midy = (p1.intensity * (p2.mz - midx) + p2.intensity * (midx - p1.mz)) / (p2.mz - p1.mz) # find the angle of the line connecting the two peaks xlo = min(p1.mz, p2.mz) xhi = max(p1.mz, p2.mz) adj = xhi - xlo ylo = min(p1.intensity, p2.intensity) yhi = max(p1.intensity, p2.intensity) opp = yhi - ylo hypot = np.hypot(adj, opp) rotation = np.arccos(adj / hypot) if isinstance(label, (list, tuple)): label = '-'.join(map(str, label)) else: label = str(label) self.ax.text(midx, midy, label, fontsize=fontsize, ha='center', va='bottom', rotation=rotation, clip_on=clip_on)
def draw_tid(composition, charge, ax=None): tid = brainpy.isotopic_variants(composition, charge=charge) if ax is None: fig, ax = plt.subplots(1) ax = draw_peaklist(tid, ax=ax) lo, hi = ax.get_xlim() lo -= 0.5 hi += 0.5 ax.set_xlim(lo, hi) return ax
def annotate_spectrum(peaks, annotated_peaks, mz_region_start=120, mz_region_end=3000): ax = draw_peaklist(peaks, alpha=0.5) upper = max(ax.get_ylim()) for solution in annotated_peaks: draw_peaklist(solution.fit.theoretical, alpha=0.8, ax=ax, color='red') y = max(p.intensity for p in solution.fit.experimental) y = min(y + 2000, upper * 0.8) label = "%s" % sorted(solution.solution.name.split("|"), key=len)[0] if solution.charge > 1: label += "$^{%d}$" % solution.charge ax.text(solution.mz, y, label, rotation=90, va='bottom', ha='center', fontsize=16) ax.set_xlim(mz_region_start, mz_region_end) max_xticks = 500 xloc = plt.MaxNLocator(max_xticks) ax.xaxis.set_major_locator(xloc) for tl in ax.get_xticklabels(): tl.set(rotation=90) fig = ax.get_figure() fig.set_figwidth(128) fig.set_figheight(64) return ax
def format_axes(self): draw_peaklist([], self.ax, pretty=True) self.ax.set_ylim(0, self.upper)
def draw_envelope_subgraph(envelopes, scale_factor=1.0, overlap_fn=peak_overlap, ax=None, **kwargs): layers = layout_layers(envelopes) max_score = max(e.score for e in envelopes) peaks = set() for e in envelopes: peaks.update(e.fit.experimental) peaks = sorted(peaks, key=lambda x: x.mz) peaks = [p.clone() for p in peaks] total_intensity = sum(p.intensity for p in peaks) start = peaks[0].mz end = peaks[-1].mz if ax is None: figure, ax = plt.subplots(1, 1) row_width = float('inf') annotation_text_size = 3. * scale_factor layer_height = 0.56 * scale_factor y_step = (layer_height + 0.05) * - scale_factor origin_y = cur_y = -layer_height - 0.075 cur_position = peaks[0].mz for layer in layers: layer.sort(key=lambda x: x.start) while cur_position < end: next_row = cur_position + row_width for layer in layers: c = 0 for envelope in layer: if envelope.start < cur_position: continue elif envelope.start > next_row: break c += 1 rect = mpatches.Rectangle( (envelope.start - 0.01, cur_y), width=0.01 + envelope.end - envelope.start, height=layer_height, facecolor='lightblue', edgecolor='black', linewidth=0.15, alpha=min(max(envelope.score / max_score, 0.2), 0.8)) ax.add_patch(rect) text_path = TextPath( (envelope.start + 0.1, cur_y + 0.2), "%0.2f, %d" % (envelope.score, envelope.fit.charge), size=annotation_text_size / 14.5, prop=font_options, stretch=200) patch = mpatches.PathPatch(text_path, facecolor='grey', lw=0.04) ax.add_patch(patch) if c > 0: cur_y += y_step cur_y += y_step / 5 cur_position = next_row for p in peaks: p.intensity = (p.intensity / total_intensity) * abs(origin_y - cur_y) * 8 draw_peaklist(peaks, ax=ax) ax.set_ylim(cur_y, max(p.intensity for p in peaks) + 0.2) ax.set_xlim(start - 0.2, end + 0.2) ax.axes.get_yaxis().set_visible(False) return ax
def format_axes(self): draw_peaklist([], self.ax, pretty=True) self.ax.set_ylim(0, self.upper)
def _draw_whole_spectrum(self): ax = draw_peaklist(self.peaklist, lw=0.25, alpha=0.5) self.ax = ax return ax