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 format_axes(in_ax: matplotlib.axes,
labelsize: int = 12,
ticksize: int = 10,
legendsize: int = 8,
box: bool = False) -> None:
"""Formats ticks, tick label sizes, and axes label sizes for box plots.
Parameters
----------
in_ax : matplotlib.axes
Axes containing a plot.
labelsize : int, optional
Size of axes labels.
ticksize : int, optional
Size of tick labels.
legendsize : int, optional
Specifies font size of strings in legend.
box : bool, optional
Specifies whether or not a box plot has been plotted.
Returns
-------
None
"""
in_ax.xaxis.set_minor_locator(AutoMinorLocator())
in_ax.yaxis.set_minor_locator(AutoMinorLocator())
in_ax.xaxis.label.set_size(labelsize)
in_ax.yaxis.label.set_size(labelsize)
in_ax.tick_params(axis='both',
which='major',
direction='in',
length=4,
bottom=True,
top=True,
left=True,
right=True,
labelsize=ticksize,
color='grey')
in_ax.tick_params(axis='both',
which='minor',
direction='in',
length=2,
bottom=True,
top=True,
left=True,
right=True,
color='grey')
if not box:
legend = in_ax.legend(fontsize=legendsize,
edgecolor=(1, 1, 1, 0.),
facecolor=(1, 1, 1, 0))
legend.get_frame().set_alpha(0)
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