def xic_detail(request, dataset_pk, mcfid, adduct_pk):
dataset = get_object_or_404(Dataset, pk=dataset_pk)
standard = get_object_or_404(Standard, inventory_id=mcfid)
adduct = get_object_or_404(Adduct, pk=adduct_pk)
mz = standard.molecule.get_mz(adduct)
delta_mz = mz * dataset.mass_accuracy_ppm * 1e-6
# xics=Xic.objects.all().filter(dataset=dataset).filter(mz__gte=mz-delta_mz).filter(mz__lte=mz+delta_mz)
xic = Xic.objects.all().filter(standard=standard,
adduct=adduct,
dataset=dataset)[0]
frag_specs = FragmentationSpectrum.objects.all().filter(
dataset=dataset).filter(precursor_mz__gte=mz - delta_mz).filter(
precursor_mz__lte=mz + delta_mz).order_by('-ms1_intensity')[:10]
form = FragSpecReview(request.POST or None,
extra=list([fs.pk for fs in frag_specs]),
user=request.user)
if form.is_valid():
for (fragSpecId, response) in form.get_response():
# todo update fields in frag spectra
logging.debug((form.user, fragSpecId, response))
tools.update_fragSpec(fragSpecId, response, standard, adduct,
request.user.username)
return redirect('dataset-detail', dataset_pk)
else:
data = {
'form':
form,
'extra': {
'x_is_date': False,
'x_axis_format': '',
'tag_script_js': True,
'jquery_on_ready': True,
},
"mz":
mz,
"dataset":
dataset,
"standard":
standard,
"adduct":
adduct,
"xic":
xic,
"frag_specs":
frag_specs,
"xic_plot":
plots.xic_plot(xic.rt, xic.xic,
[spectrum.rt for spectrum in frag_specs],
[spectrum.ms1_intensity
for spectrum in frag_specs]),
"frag_info":
zip(frag_specs, [
plots.fragment_plot(
spectrum.centroid_mzs, spectrum.centroid_ints,
spectrum.precursor_mz) for spectrum in frag_specs
])
}
return render(request,
'mcf_standards_browse/mcf_xic_detail.html',
context=data)
def molecule_detail(request, pk):
molecule = get_object_or_404(Molecule, pk=pk)
standards = Standard.objects.all().filter(molecule=molecule)
frag_specs = []
for standard in standards:
frag_specs.extend(FragmentationSpectrum.objects.all().filter(standard=standard))
chart_type = 'line'
chart_height = 300
_frag_specs = []
for standard in standards:
_frag_specs.append(
[(spectrum, plots.fragment_plot(spectrum.centroid_mzs, spectrum.centroid_ints, spectrum.precursor_mz))
for spectrum in FragmentationSpectrum.objects.all().filter(standard=standard)] )
data = {
'molecule': molecule,
"standards": zip(standards, _frag_specs),
"frag_spec_highchart": [{
"chart_id": 'frag_spec{}'.format(spec.id),
"chart": {"type": chart_type, "height": chart_height, "zoomType": "x"},
"title": {"text": ''},
"xAxis": {"title": {"text": 'm/z'},},
"yAxis": {"title": {"text": 'Intensity'}},
"series": [
{"name": 'fragment spectrum', "data": [[x + d, y * m] for x, y in
zip(np.round(spec.centroid_mzs, 5),
spec.centroid_ints) for d, m in
zip([-0.00, 0, 0.00], [0, 1, 0])]
},
],} for spec in frag_specs],
}
return render(request, 'mcf_standards_browse/mcf_molecule_detail.html', data)
def standard_detail(request, mcfid):
standard = get_object_or_404(Standard, inventory_id=mcfid)
frag_specs = FragmentationSpectrum.objects.all().filter(standard=standard)
xics = Xic.objects.all().filter(standard=standard)
xic_plots = ""
if frag_specs:
xic_plots = plots.multixic([
(xic.rt, xic.xic, [spectrum.rt for spectrum in frag_specs],
[spectrum.ms1_intensity for spectrum in frag_specs])
for xic in xics
])
data = {
'extra': {
'x_is_date': False,
'x_axis_format': '',
'tag_script_js': True,
'jquery_on_ready': True,
},
"standard":
standard,
"xics":
xics,
"frag_specs":
frag_specs,
"xic_plot":
xic_plots,
"frag_info":
zip(frag_specs, [
plots.fragment_plot(spectrum.centroid_mzs, spectrum.centroid_ints,
spectrum.precursor_mz)
for spectrum in frag_specs
])
}
return render(request, 'mcf_standards_browse/mcf_standard_detail.html',
data)
def fragmentSpectrum_detail(request, pk):
spectrum = get_object_or_404(FragmentationSpectrum, pk=pk)
xic = Xic.objects.all().filter(standard=spectrum.standard, adduct=spectrum.adduct, dataset=spectrum.dataset)[0]
splash_payload = json.dumps({
"ions": [{"mass": mz, "intensity": int_} for mz, int_ in zip(spectrum.centroid_mzs, spectrum.centroid_ints)],
"type": "MS"})
data = {
'specdata': {
'spectrum': spectrum,
'centroids': [spectrum.centroid_mzs, spectrum.centroid_ints],
},
"splash_payload": splash_payload,
"fragment_plot": plots.fragment_plot(spectrum.centroid_mzs, spectrum.centroid_ints, pk),
"xic_plot": plots.xic_plot(xic.rt, xic.xic, [spectrum.rt,], [spectrum.ms1_intensity,],)
}
return render(request, 'mcf_standards_browse/mcf_fragmentSpectrum_detail.html', data)