Source code for emzed.align.mz_align

# encoding: utf-8

MMU = 0.001

[docs]def mzAlign(table, mz_reference_table, tol=15 * MMU, destination=None, minR2=0.95, maxTol=1 * MMU, minPoints=5, interactive=False): """ performs affine linear mz-correction for a feature table. and retention times of known metabolites. This table needs columns ``mz_calc`` for the mz value calculated from the mass of the isotope, ``rtmin``, ``rtmax`` for the retention time window where the peak is expected to elute from the column in order to restrict the match of the table against the ``mz_reference_table`. ``destination`` is a directory which will be used for storing the result and intermediate data. If you do not specify this value, a dialog for choosing the destination directory will be opened. The input table **is not modified** in place, the function returns the aligned table. the parameter *tol* is related to find matching peaks, *maxTol* and *minR2* determine stop criterion when removing outlier points in non interactive mode. """ import os import numpy as np from _mzalign_helpers import (_findMzMatches, _findParametersAutomatically, _findParametersManually, _plotAndSaveMatch, _applyTransform) if not interactive: assert minR2 <= 1.0 assert minPoints > 1 sources = set(table.source.values) assert len(sources) == 1 source = sources.pop() polarities = set(table.polarity.values) assert len(polarities) == 1, "multiple polarities in table" polarity = polarities.pop() hypot = mz_reference_table hypot.requireColumn("mz_hypot") hypot.requireColumn("rtmin") hypot.requireColumn("rtmax") hypot.requireColumn("name") hypot.requireColumn("polarity") polarity_hypot = hypot.getColumn("polarity").uniqueValue() assert hypot.getColType("mz_hypot") == float, "col mz_hypot is not float" assert hypot.getColType("rtmin") == float, "col rtmin is not float" assert hypot.getColType("rtmax") == float, "col rtmax is not float" assert polarity_hypot == polarity, "polarity of mz reference table (%s)"\ "does not correspond to polarity of sample tables %s" \ % (polarity_hypot, polarity) # hypot = _buildHypotheseTable(polarity, univ.copy(), fullC13) if destination is not None: basename = os.path.basename(source) fname, _ = os.path.splitext(basename), fname + "_hypot.table"), True) real, tobe, matches = _findMzMatches(hypot, table, tol) if len(real) <= 1: print "NOT ENOUGH MATCHES FOR ALIGNMENT" return if interactive: from .. import gui gui.inspect(matches, offerAbortOption=True) elif len(tobe) < minPoints: raise Exception("could only match %d peaks" % len(tobe)) if not interactive: transform, used = _findParametersAutomatically(tobe.copy(), real.copy(), minR2, maxTol, minPoints) else: transform, used = _findParametersManually(tobe.copy(), real.copy()) if transform is None: print "ABORTED" return if destination is not None: matches.addColumn("error", np.linalg.norm(transform(real) - tobe), float, "%.3e"), fname + "_mzalign.table"), True) matches.storeCSV(os.path.join(destination, fname + "_mzalign.csv")) path = os.path.join(destination, fname + "_mzalign.png") _plotAndSaveMatch(tobe, real, used, transform, path) transformedTable = _applyTransform(table, transform) print "DONE" return transformedTable