def makePowerSpectrum(
self, freqs: np.array, power: np.array, sm_power: np.array,
band_max_power: float, freq_at_band_max_power: float,
max_freq: int = 50, theta_range: tuple = [6, 12],
ax: matplotlib.axes = None, **kwargs) -> matplotlib.axes:
# downsample frequencies and power
freqs = freqs[0::50]
power = power[0::50]
sm_power = sm_power[0::50]
if ax is None:
fig = plt.figure()
ax = fig.add_subplot(111)
ax.plot(freqs, power, alpha=0.5, color=[0.8627, 0.8627, 0.8627])
ax.plot(freqs, sm_power)
ax.set_xlim(0, max_freq)
ylim = [0, band_max_power / 0.8]
if 'ylim' in kwargs:
ylim = kwargs['ylim']
ax.set_ylim(ylim)
ax.set_ylabel('Power')
ax.set_xlabel('Frequency')
ax.text(
x=theta_range[1] / 0.9, y=band_max_power,
s=str(freq_at_band_max_power)[0:4], fontsize=20)
from matplotlib.patches import Rectangle
r = Rectangle((
theta_range[0], 0), width=np.diff(theta_range)[0],
height=np.diff(ax.get_ylim())[0], alpha=0.25, color='r', ec='none')
ax.add_patch(r)
return ax
def show_reference(
query_record: SeqRecord,
subject_record: SeqRecord,
ax: mpl.axes,
ref_central: Optional[int] = None,
) -> mpl.axes:
"""show the reference of the chromatograph.
design: if location is not proviode, do the alignment first
@param seq: input SeqRecord of ref
"""
sitepairs = align_chromatograph(
query_record, subject_record, ignore_ambig=True
)
sitepairs_indexing = {s.cf_pos: s for s in sitepairs}
cf_sites = [int(i.get_text()) for i in ax.get_xticklabels()]
matched_sitepairs = [sitepairs_indexing[pos] for pos in cf_sites]
for i, peak in enumerate(ax.get_xticks()):
ax.text(
peak,
1.05,
matched_sitepairs[i].ref_base,
color="dimgrey",
va="bottom",
ha="center",
alpha=0.85,
fontsize="xx-large",
fontweight="bold",
clip_on=False,
)
if ref_central is not None:
ref_pos = matched_sitepairs[i].ref_pos - ref_central
else:
ref_pos = matched_sitepairs[i].ref_pos
ax.text(
peak,
1.12,
ref_pos,
color="dimgrey",
va="bottom",
ha="center",
alpha=0.85,
fontsize="medium",
fontweight="normal",
clip_on=False,
)
return ax
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_visit_durations(data: list, ax: Axes):
"""
Plot the visit durations from the raw data.
:param data: Raw data
:param ax: Axes object in which to put the plot
:return: None
"""
# Histogram options
min_visit_s = 30
max_visit_s = 60 * 60 * 3
nbins = 150
# Regression line options
fit_start = 6
fit_stop = 144
# Create histogram
durations = get_visit_durations(data)
n, bins, _ = ax.hist(durations, bins=linspace(min_visit_s, max_visit_s, nbins))
# Create regression line
bin_width = (bins[fit_stop - 1] - bins[fit_start]) / (fit_start - fit_stop)
lin_fitting_bins = [b + bin_width / 2 for b in bins[fit_start:fit_stop]]
lin_fitting_n = n[fit_start:fit_stop]
[a, b] = polyfit(lin_fitting_bins, log(lin_fitting_n), 1, w=sqrt(lin_fitting_n))
fitted_n = [exp(b + a * t) for t in lin_fitting_bins]
regression_line_opts = {"linestyle": "--", "color": "black", "linewidth": 2}
regression_label_text = "y={:.0f}exp({:.6f}*t)".format(exp(b), a)
regression_label_coords = (max_visit_s * 0.6, max(n) * 0.5)
ax.plot(lin_fitting_bins, fitted_n, **regression_line_opts)
ax.text(*regression_label_coords, regression_label_text)
# Label axes
ax.set_xlabel("Varighet for visitt (s)")
ax.set_ylabel("Andel visitter (vilkårlig)")
ax.set_yscale("log")
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
