def test_plot_glycans(self):
for name, structure in glycans.items():
for layout in ['balanced', 'topological']:
for symbol_nomenclature in ['cfg']: # ['cfg', 'iupac']:
plot.plot(
structure, label=True, orientation='h',
symbol_nomenclature=symbol_nomenclature, layout=layout)
path = "%s\%s_%s_%s.png" % (plot_dir, name, layout, symbol_nomenclature)
plt.savefig(path)
plt.clf()
plt.close('all')
#os.remove(plot_dir + os.sep + name + '.png')
plt.figure()
plot.enumerate_tree(*plot.plot(glycan_structure))
plt.savefig(plot_dir + os.sep + "enum_tree" + '.png')
def cfg_plot(record):
if "svg_plot" in record.report_data:
return base64.decodestring(record.report_data["svg_plot"])
s = record.structure.clone()
composition_transform.strip_derivatization(s)
dtree, ax = plot.plot(s, orientation='h', squeeze=1.4, scale=.135)
fmap = {f.name: f for f in record.fragments}
for match in record.matches:
match_key = match.match_key.split(":")[0]
order = len(match_key.split("-"))
if order == 1:
dtree.draw_cleavage(ax=ax, fragment=fmap[match_key], color='red', label=True)
else:
for key in match_key.split("-"):
dtree.draw_cleavage(fragment=fmap[key], ax=ax, color='orange', label=True)
ax.axis('off')
fig = ax.get_figure()
fig.tight_layout(pad=0.2)
img_buffer = StringIO()
fig.savefig(img_buffer, format="svg")
plt.close(fig)
root, ids = ET.XMLID(img_buffer.getvalue())
root.set("id", dtree.uuid)
svg = ET.tostring(root)
record.report_data["svg_plot"] = base64.encodestring(svg)
record.update()
return svg
def simple_plot(record):
dtree, ax = plot.plot(record, orientation='h', squeeze=1.4, scale=.135)
ax.axis('off')
fig = ax.get_figure()
fig.tight_layout(pad=0.2)
img_buffer = StringIO()
fig.savefig(img_buffer, format="svg")
plt.close(fig)
root, ids = ET.XMLID(img_buffer.getvalue())
root.set("id", dtree.uuid)
svg = ET.tostring(root)
return svg
def parsePlot(linear_code_expression):
'''
Abbreviation for
`plot(glypy.io.linear_code.parse_linear_code(linear_code_expression))`
'''
plot(glypy.io.linear_code.parse_linear_code(linear_code_expression))
def test_plot_monosaccharide(self):
for name, residue in monosaccharides.items():
plot.plot(residue)
#plt.savefig(plot_dir + os.sep + name + '.png')
plt.clf()
plt.close('all')
