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')