def _plotIDStrip(ax: matplotlib.axes, id_array: np.ndarray, label: str,
x_extents: List[float]) -> None:
'''
Plot a strip above the data sequence image that represents class labels at each time.
'''
id_array = np.reshape(id_array, (1, len(id_array)))
ax.imshow(id_array, aspect="auto", interpolation="none", extent=x_extents + [0, 1])
ax.set_ylabel(label)
ax.get_xaxis().set_visible(False)
ax.get_yaxis().set_ticks([])
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