def plot_compounds(self, qc_corrected_file, plot_location):
""" plot a list of compounds """
# load measurements file
mea = Mea(mea_file=qc_corrected_file)
# init plot class
qcplot = Qcplot(mea=mea)
# plot the compound
for compound in mea.get_compounds():
qcplot.plot_compound_qc_data(compound=compound,
location=plot_location)
def export_measurements(self,
file,
column,
export_location,
include_is=False):
""" exports data as samples vs compounds"""
# load measurements file
mea = Mea(file)
# store as table
mea.as_table(column=column,
location=export_location,
include_is=include_is)
def summary(self, mea_file):
""" Report a summary of the measurements ... """
try:
# load measurements file
mea = Mea(mea_file)
# build summary dict
summary = {
'batches': mea.get_batches().tolist(),
'samples': mea.get_samples().tolist(),
'compounds': mea.get_compounds().tolist()
}
except:
summary = {}
# return a json encoded dict
return json.JSONEncoder().encode(summary)
def plot_compound(self, qc_corrected_file, compound, plot_location):
""" plot an individual compound """
# load measurements file
mea = Mea(mea_file=qc_corrected_file)
# init plot class
qcplot = Qcplot(mea=mea)
# plot the compound
qcplot.plot_compound_qc_data(compound=compound, location=plot_location)
def plot_compounds_zipped(self, qc_corrected_file, zip_file):
""" plot a list of compounds and store them as a zip file """
# load measurements file
mea = Mea(mea_file=qc_corrected_file)
# init plot class
qcplot = Qcplot(mea=mea)
# plot the compound
with tempfile.TemporaryDirectory() as tmpdir:
for compound in mea.get_compounds():
qcplot.plot_compound_qc_data(compound=compound,
location=tmpdir)
zipf = zipfile.ZipFile(zip_file, 'w', zipfile.ZIP_DEFLATED)
for root, dirs, files in os.walk(tmpdir):
for file in files:
if not os.path.isdir(file) and file.split(
'.')[-1].lower() == 'html':
zipf.write(os.path.join(root, file), file)
zipf.close()
def rep_rsd(self, qc_corrected_file, rep_rsd_file, by_batch=False):
""" Calculate the Replicate RSD's ... """
# load measurements file
mea = Mea(qc_corrected_file)
# init calc class
qccalc = Qccalc(mea=mea)
# calculate qc rsd's
rsdrep = qccalc.rsdrep(by_batch=by_batch)
# save results to file
rsdrep.to_csv(rep_rsd_file, sep="\t", index=False, encoding='utf-8')
def qc_correction(self, mea_file, qc_corrected_file):
""" Calculate the QC corrected data ... """
# load measurements file
mea = Mea(mea_file)
# init calc class
qccalc = Qccalc(mea=mea)
# calculate qc corrected data
qc_corrected = qccalc.qc_correction()
# save results to file
qc_corrected.to_csv(qc_corrected_file,
sep="\t",
index=False,
encoding='utf-8')
def rt_shifts(self, mea_file, rt_shifts_file):
""" Calculate the RT shifts of each compound per batch ... """
# load measurements file
mea = Mea(mea_file)
# init calc class
qccalc = Qccalc(mea=mea)
# calculate qc rsd's
rt_shifts = qccalc.rt_shifts()
# save results to file
rt_shifts.to_csv(rt_shifts_file,
sep="\t",
index=False,
encoding='utf-8')
def blank_effect(self, mea_file, blank_effect_file, by_batch=False):
""" Calculate the blank effect of ... """
# load measurements file
mea = Mea(mea_file)
# init calc class
qccalc = Qccalc(mea=mea)
# calculate blank effect
blank_effect = qccalc.blank_effect(by_batch=by_batch)
# save results to file
blank_effect.to_csv(blank_effect_file,
sep="\t",
index=False,
encoding='utf-8')
def internal_standard_rsd(self,
qc_corrected_file,
is_rsd_file,
by_batch=False):
""" Calculate the Internal Standard RSD's ... """
# load measurements file
mea = Mea(qc_corrected_file)
# init calc class
qccalc = Qccalc(mea=mea)
# calculate qc rsd's
rsdis = qccalc.rsdis(by_batch=by_batch)
# save results to file
rsdis.to_csv(is_rsd_file, sep="\t", index=False, encoding='utf-8')