def _make_histogram(data, axis_labels, nbins, barcolor):
"""Create a fig, ax instance and generate a histogram.
:param data: np.array
:param axis_labels: (tuple of str) (axis label, y axis label)
:return: matplotlib fig, ax
"""
# axis_labels = ('Median Distance Between Adapters', 'Pre-Filter Reads')
fig, ax = get_fig_axes_lpr()
apply_histogram_data(ax, data, nbins, axis_labels=axis_labels, barcolor=barcolor)
return fig, ax
def _make_histogram(datum, axis_labels, nbins, barcolor):
"""Create a fig, ax instance and generate a histogram.
:param datum: np.array
:param axis_labels: (tuple of str) (axis label, y axis label)
:return: matplotlib fig, ax
"""
# axis_labels = ('Median Distance Between Adapters', 'Pre-Filter Reads')
fig, ax = get_fig_axes_lpr()
apply_histogram_data(ax, datum, nbins, axis_labels=axis_labels,
barcolor=barcolor)
return fig, ax
def _create_histogram(stats):
"""
Returns a fig,ax histogram plot for this reference
:param stats: (ReferenceStats)
"""
numBins = 100
binSize = max(1, int(stats.maxbin / numBins))
# handle case where the coverage is zero. This prevents the histogram
# construction from crashing with an index error.
m = 1 if stats.maxbin == 0.0 else stats.maxbin
bins = np.arange(0, m, binSize)
fig, ax = get_fig_axes_lpr()
apply_histogram_data(ax, stats.means, bins,
('Coverage', 'Reference Regions'),
barcolor=Constants.COLOR_STEEL_BLUE_DARK,
showEdges=False)
return fig, ax
def _create_histogram(self, stats):
"""
Returns a fig,ax histogram plot for this reference
:param stats: (ReferenceStats)
"""
numBins = 100
binSize = max(1, int(stats.maxbin / numBins))
# handle case where the coverage is zero. This prevents the histogram
# construction from crashing with an index error.
m = 1 if stats.maxbin == 0.0 else stats.maxbin
bins = np.arange(0, m, binSize)
fig, ax = get_fig_axes_lpr()
xlabel = get_plot_xlabel(self.spec, Constants.PG_COVERAGE_HIST,
Constants.P_COVERAGE_HIST)
ylabel = get_plot_ylabel(self.spec, Constants.PG_COVERAGE_HIST,
Constants.P_COVERAGE_HIST)
apply_histogram_data(ax, stats.means, bins, (xlabel, ylabel),
barcolor=Constants.COLOR_STEEL_BLUE_DARK,
showEdges=False)
return fig, ax
def test_save_histograms(self):
"""Save std histograms."""
tmpdir = tempfile.mkdtemp(prefix='pbreport_output')
fig, ax = get_fig_axes_lpr()
dump = os.path.join(tmpdir, 'dmp.data')
log.debug('dmp file is {d}'.format(d=dump))
apply_histogram_data(ax, [1, 2, 3, 4, 5, 6], 2,
axis_labels=('foo', 'bar'),
barcolor='#505050', xlim=(0, 20000),
data_file=dump)
self.assertTrue(os.path.exists(dump))
log.info("Writing temp histogram to {t}".format(t=tmpdir))
save_figure_with_thumbnail(fig, os.path.join(tmpdir, 'foo.png'))
self.assertTrue(os.path.exists(os.path.join(tmpdir, 'foo.png')))
self.assertTrue(os.path.exists(os.path.join(tmpdir, 'foo_thumb.png')))
def test_save_histograms(self):
"""Save std histograms."""
tmpdir = tempfile.mkdtemp(prefix='pbreport_output')
fig, ax = get_fig_axes_lpr()
dump = os.path.join(tmpdir, 'dmp.data')
log.debug('dmp file is {d}'.format(d=dump))
apply_histogram_data(ax, [1, 2, 3, 4, 5, 6], 2,
axis_labels=('foo', 'bar'),
barcolor='#505050', xlim=(0, 20000),
data_file=dump)
self.assertTrue(os.path.exists(dump))
log.info("Writing temp histogram to {t}".format(t=tmpdir))
save_figure_with_thumbnail(fig, os.path.join(tmpdir, 'foo.png'))
self.assertTrue(os.path.exists(os.path.join(tmpdir, 'foo.png')))
self.assertTrue(os.path.exists(os.path.join(tmpdir, 'foo_thumb.png')))
