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 highlight_base(
pos_highlight: int, seq: SeqRecord, ax: mpl.axes, passed_filter=True
) -> mpl.axes:
"""Highlight the area around a peak with a rectangle."""
peaks = seq.annotations["peak positions"]
peak = peaks[pos_highlight - 1]
xmin, xmax = ax.get_xlim()
if not xmin <= peak < xmax:
raise ValueError("peak not within plot bounds")
if pos_highlight == 1:
xmin = -0.5
else:
xmin = 0.5 * (peaks[pos_highlight - 1] + peaks[pos_highlight - 2])
if pos_highlight == len(peaks):
xmax = -0.5
else:
xmax = 0.5 * (peaks[pos_highlight - 1] + peaks[pos_highlight])
ymin, ymax = ax.get_ylim()
if passed_filter:
fcolor = "yellow"
else:
fcolor = "grey"
rec = mpl.patches.Rectangle(
(xmin, ymin),
(xmax - xmin),
(ymax - ymin),
edgecolor="none",
facecolor=fcolor,
alpha=0.3,
)
ax.add_patch(rec)
return ax
