def draw_hist(self, fhand):
scores = self._scores
titles = ['aaaa'] * len(scores)
plots_per_chart = 3
num_cols = 2 if len(scores) > plots_per_chart else 1
plot = HistogramPlotter(scores.values(), ylabel='Num. SNPs',
xlabel='Coverage', titles=titles, kind=LINE,
distrib_labels=scores.keys(),
num_cols=num_cols,
plots_per_chart=plots_per_chart)
for axe in plot.axes:
axe.axvline(self._coverage_threshold)
plot.write_figure(fhand)
def draw_hist(self, fhand):
scores = self._scores
titles = ['aaaa'] * len(scores)
plots_per_chart = 3
num_cols = 2 if len(scores) > plots_per_chart else 1
plot = HistogramPlotter(scores.values(), ylabel='Num. SNPs',
xlabel='Coverage', titles=titles, kind=LINE,
distrib_labels=scores.keys(),
num_cols=num_cols,
plots_per_chart=plots_per_chart)
for axe in plot.axes:
axe.axvline(self._coverage_threshold)
plot.write_figure(fhand)
def test_histogram_plotter(self):
values = [1, 2, 3, 1, 2, 3, 2, 3, 2, 3, 2, 1, 4]
counter = IntCounter(values)
counters = [counter]
histo_ploter = HistogramPlotter(counters)
assert len(histo_ploter.axes) == len(counters)
fhand = NamedTemporaryFile(suffix='.png')
histo_ploter.write_figure(fhand)
# raw_input(fhand.name)
# Add more intcounters
counters.append(IntCounter(values))
counters.append(IntCounter(values))
histo_ploter = HistogramPlotter(counters,
distrib_labels=['1', '2', '3'])
assert len(histo_ploter.axes) == len(counters)
def test_histogram_plotter(self):
values = [1, 2, 3, 1, 2, 3, 2, 3, 2, 3, 2, 1, 4]
counter = IntCounter(values)
counters = [counter]
histo_ploter = HistogramPlotter(counters)
assert len(histo_ploter.axes) == len(counters)
fhand = NamedTemporaryFile(suffix='.png')
histo_ploter.write_figure(fhand)
# raw_input(fhand.name)
# Add more intcounters
counters.append(IntCounter(values))
counters.append(IntCounter(values))
histo_ploter = HistogramPlotter(counters,
distrib_labels=['1', '2', '3'])
assert len(histo_ploter.axes) == len(counters)
def draw_hist(self, fhand):
counters = self._scores.values()
samples = self._scores.keys()
titles = ['Genotype quality distribution'] * len(counters)
plots_per_chart = 3
num_cols = 1 if len(counters) <= plots_per_chart else 2
plot = HistogramPlotter(counters,
distrib_labels=samples,
xlabel='Genotype quality',
num_cols=num_cols,
ylabel='num genotypes',
titles=titles,
plots_per_chart=plots_per_chart)
for axe in plot.axes:
axe.axvline(self._min_qual, linewidth=2, c='#FF8D00')
plot.write_figure(fhand)
def draw_hist(self, fhand):
counters = self._scores.values()
samples = self._scores.keys()
titles = ["Genotype quality distribution"] * len(counters)
plots_per_chart = 3
num_cols = 1 if len(counters) <= plots_per_chart else 2
plot = HistogramPlotter(
counters,
distrib_labels=samples,
xlabel="Genotype quality",
num_cols=num_cols,
ylabel="num genotypes",
titles=titles,
plots_per_chart=plots_per_chart,
)
for axe in plot.axes:
axe.axvline(self._min_qual, linewidth=2, c="#FF8D00")
plot.write_figure(fhand)