def makeXCorr(self, spk_times: np.array, ax: matplotlib.axes = None, **kwargs) -> matplotlib.axes: # spk_times in samples provided in seconds but convert to # ms for a more display friendly scale spk_times = spk_times / 3e4 * 1000. S = SpikeCalcsGeneric(spk_times) y = S.xcorr(spk_times) if ax is None: fig = plt.figure() ax = fig.add_subplot(111) ax.hist( y[y != 0], bins=201, range=[-500, 500], color='k', histtype='stepfilled') ax.set_xlim(-500, 500) ax.set_xticks((-500, 0, 500)) ax.set_xticklabels('') ax.tick_params( axis='both', which='both', left=False, right=False, bottom=False, top=False) ax.set_yticklabels('') ax.spines['right'].set_visible(False) ax.spines['top'].set_visible(False) ax.spines['left'].set_visible(False) ax.xaxis.set_ticks_position('bottom') return ax
def plot_openness_by_hour(data: list, period: dict, ax: Axes): """ Plots the openness by hour from the raw data. :param data: Raw data :param period: Period over which to average the openness :param ax: Axes object in which to put the plot :return: None """ num_hrs = 24 # Get data hour_bins = get_openness_by_hour(data, period) # Plot bar chart ax.bar(range(num_hrs + 1), hour_bins) # Decorate the axes ax.yaxis.grid(True, which="both", linestyle="-.") ax.set_xlim(1, num_hrs) ax.set_xticks(range(num_hrs + 1)) ax.set_xticklabels([f"{t:02d}" for t in ax.get_xticks()]) ax.set_yticklabels([f"{o * 100:.1f}{percent()}" for o in ax.get_yticks()]) ax.set_ylabel("Andel åpen") ax.set_xlabel("Tid på døgnet")
def plot_openness_by_weekday_by_semester(period: dict, ax: Axes): """ Plot openness by semester. :param period: Period over which to average the openness :param ax: Axes object in which to put the plot :return: None """ # Configuration num_weekdays = 5 init_year = 2015 init_semester = "Vår" # Get data for plot dataseries = get_openness_by_weekday_by_semester(period) num_series = len(dataseries) bar_width = 1 / (num_series + 1) # Create plot cur_year = init_year cur_semester = init_semester legend = [] for semester_index, week_bins in enumerate(dataseries): # Add bars ax.bar( [ weekday_index + semester_index * bar_width for weekday_index in range(num_weekdays) ], height=week_bins[:num_weekdays], width=bar_width, ) # Add to legend legend.append(f"{cur_semester} {cur_year}") # Update semester and year for next bars if cur_semester == "Høst": cur_semester = "Vår" cur_year += 1 else: cur_semester = "Høst" # Place legend and labels ax.legend(legend, loc="lower right") ax.set_xticklabels(("", "Mandag", "Tirsdag", "Onsdag", "Torsdag", "Fredag")) ax.set_yticklabels( [f"{openness * 100:.1f}{percent()}" for openness in ax.get_yticks()] ) ax.set_ylabel("Andel åpen")
def plot_openness(data: list, period: dict, ax: Axes): """ Plots the openness from the raw data. :param data: Raw data :param period: Period over which to average the openness :param ax: Axes object in which to put the plot :return: None """ # Get data datetimes, openness = get_openness(data, period) # Make filled line plot ax.fill_between(datetimes, openness) # Decorate axes ax.xaxis.set_major_locator(MonthLocator((1, 4, 7, 10), bymonthday=1)) ax.xaxis.set_major_formatter(DateFormatter("%b '%y")) ax.set_yticklabels([f"{o * 100:.0f}{percent()}" for o in ax.get_yticks()]) ax.set_ylabel("Andel åpen") ax.grid(linestyle="-.")
def plot_openness_by_weekday(data: list, period: dict, ax: Axes): """ Plot the openness by weekday from the raw data. :param data: Raw data :param period: Period over which to average the openness :param ax: Axes object in which to put the plot :return: None """ week_bins = get_openness_by_weekday(data, period) weekday_avg = sum(week_bins[0:5]) / 5 weekend_avg = sum(week_bins[5:7]) / 2 # Plot bar ax.bar(range(7), week_bins) # Plot averages ax.text( 2, weekday_avg * 1.05, f"Gjennomsnitt ukedager: {weekday_avg * 100:.0f}{percent()}", ) ax.text( 4.5, weekend_avg * 1.1, f"Gjennomsnitt helgedager: {weekend_avg * 100:.0f}{percent()}", ) ax.plot((0, 5 - 1), (weekday_avg, weekday_avg), "k--") ax.plot((5, 7 - 1), (weekend_avg, weekend_avg), "k--") # Decorate axes ax.set_xticklabels( ("", "Mandag", "Tirsdag", "Onsdag", "Torsdag", "Fredag", "Lørdag", "Søndag") ) ax.set_yticklabels( [f"{openness * 100:.1f}{percent()}" for openness in ax.get_yticks()] ) ax.set_ylabel("Andel åpen")
def plot_chromatograph( seq: SeqRecord, region: Tuple[int, int] = None, ax: mpl.axes = None ) -> plt.axes: """Plot Sanger chromatograph. region: include both start and end (1-based) """ if seq is None: return ax if region is None: # turn into 0 based for better indexing region_start, region_end = 0, len(seq) else: region_start = max(region[0], 0) region_end = min(region[1], len(seq) - 1) if ax is None: _, ax = plt.subplots(1, 1, figsize=(16, 6)) _colors = defaultdict( lambda: "purple", {"A": "g", "C": "b", "G": "k", "T": "r"} ) # Get signals peaks = seq.annotations["peak positions"] trace_x = seq.annotations["trace_x"] traces_y = [seq.annotations["channel " + str(i)] for i in range(1, 5)] bases = seq.annotations["channels"] xlim_left, xlim_right = peaks[region_start] - 1, peaks[region_end] + 0.5 # subset peak and sequence # TODO: this might fix the bug peak_start = peaks[0] peak_zip = [ (p, s) for i, (p, s) in enumerate(zip(peaks, seq)) if region_start <= i <= region_end ] peaks, seq = list(zip(*peak_zip)) # subset trace_x and traces_y together trace_zip = [ (x + peak_start, *ys) for x, *ys in zip(trace_x, *traces_y) if xlim_left <= x <= xlim_right ] if not trace_zip: return ax trace_x, *traces_y = list(zip(*trace_zip)) # Plot traces trmax = max(map(max, traces_y)) for base in bases: trace_y = [1.0 * ci / trmax for ci in traces_y[bases.index(base)]] ax.plot(trace_x, trace_y, color=_colors[base], lw=2, label=base) ax.fill_between( trace_x, 0, trace_y, facecolor=_colors[base], alpha=0.125 ) # Plot bases at peak positions for i, peak in enumerate(peaks): # LOGGER.debug(f"{i}, {peak}, {seq[i]}, {xlim_left + i}") ax.text( peak, -0.11, seq[i], color=_colors[seq[i]], va="center", ha="center", alpha=0.66, fontsize="x-large", fontweight="bold", ) ax.set_ylim(bottom=-0.15, top=1.05) # peaks[0] - max(2, 0.02 * (peaks[-1] - peaks[0])), # right=peaks[-1] + max(2, 0.02 * (peaks[-1] - peaks[0])), ax.set_xlim(xlim_left + 0.5, xlim_right) ax.set_xticks(peaks) ax.set_xticklabels(list(range(region_start + 1, region_end + 2))) # hide y axis ax.set_yticklabels([]) ax.get_yaxis().set_visible(False) # hide border ax.spines["left"].set_visible(False) ax.spines["right"].set_visible(False) ax.spines["top"].set_visible(False) # hide grid ax.grid(False) # set legend ax.legend(loc="upper left", bbox_to_anchor=(0.95, 0.99)) return ax