nomspectra.recal module

class nomspectra.recal.ErrorTable(table: Optional[pandas.core.frame.DataFrame] = None)[source]

Bases: object

A class used to recallibrate mass spectrum

__init__(table: Optional[pandas.core.frame.DataFrame] = None) → None[source]

Init ErrorTable object

Parameters

table (pandas Datarame) – consist error table: error in ppm for mass

static assign_error(spec: nomspectra.spectrum.Spectrum, ppm: float = 3, brutto_dict={'C': (4, 30), 'H': (4, 60), 'O': (0, 20)}, mode='-', show_map: bool = True)[source]

Recallibrate by assign error

Parameters

  • spec (Spectrum object) – Initial mass spectrum for recallibrate

  • ppm (float) – Permissible relative error in callibrate error. Default 3.

  • brutto_dict (dict) – Dictonary with elements ranges for assignment

  • mode (str) – Optional. Default ‘-’ negative mode. May be +, - or 0

  • show_error (bool) – Optional. Default True. Show process

Return type

ErrorTable

static etalon_error(spec: nomspectra.spectrum.Spectrum, etalon: nomspectra.spectrum.Spectrum, quart: float = 0.9, ppm: float = 3, show_map: bool = True)[source]

Recallibrate by etalon

Parameters

  • spec (Spectrum object) – Initial mass spectrum for recallibrate

  • etalon (Spectrum object) – Etalon mass spectrum

  • quart (float) – Optionaly. by default it is 0.9. Usualy it is enough for good callibration Quartile, which will be taken for calc recallibrate error

  • ppm (float) – Optionaly. Default 3. permissible relative error in ppm for seak peak in etalon

  • show_map (bool) – Optional. Default True. Show process

Return type

ErrorTable

extrapolate(ranges: Optional[Tuple[float, float]] = None) → nomspectra.recal.ErrorTable[source]

Extrapolate error data

Parameters

ranges (Tuple(numeric, numeric)) – Optionaly. Default None - all width of mass in error table. For which diaposone of mass extrapolate data

Return type

ErrorTable

static fit_kernel(f: numpy.array, mass: numpy.array, err_ppm: float = 3, show_map: bool = True) → pandas.core.frame.DataFrame[source]

Fit max intesity of kernel density map

Parameters

  • f (np.array) – keerndel density map in numpy array 100*100

  • show_map (bool) – Optional. Default true. Plot how fit kernel

Return type

Pandas Dataframe

static kernel_density_map(df_error: pandas.core.frame.DataFrame, ppm: float = 3) → numpy.array[source]

Calculate and plot kernel density map 100*100 for data

Parameters

  • df_error (pd.Dataframe) – error_table for generate kerle density map

  • ppm (float) – Optional. Default 3. treshould for generate

  • show_map (bool) – Optional. Default False. plot kde

Return type

numpy array

static massdiff_error(spec: nomspectra.spectrum.Spectrum, show_map: bool = True)[source]

Self-recallibration of mass-spectra by mass-difference map

Parameters

  • spec (Spectrum object) – Initial mass spectrum for recallibrate

  • show_error (bool) – Optional. Default True. Show process

Return type

ErrorTable

References

Smirnov, K. S., Forcisi, S., Moritz, F., Lucio, M., & Schmitt-Kopplin, P. (2019). Mass difference maps and their application for the recalibration of mass spectrometric data in nontargeted metabolomics. Analytical chemistry, 91(5), 3350-3358.

static md_error_map(spec: nomspectra.spectrum.Spectrum, ppm: float = 3) → pandas.core.frame.DataFrame[source]

Calculate mass differnce map

Parameters

  • spec (Spectrum) – data

  • ppm (float) – Optional. Default 3. Permissible error in ppm

  • show_map (bool) – Optional. Default False. Show error in ppm versus mass

Return type

Pandas Dataframe

show_error() → None[source]

Plot error map from ErrorTable class data

nomspectra.recal.recallibrate(spec: nomspectra.spectrum.Spectrum, error_table: Optional[nomspectra.recal.ErrorTable] = None, how: str = 'assign', mode: str = '-', draw: bool = True) → nomspectra.spectrum.Spectrum[source]

Recallibrate spectrum

Fine reccalabration based on self (assign or mass differnce map) or with external ethalon spectrum

Parameters

  • spec (Spectrum object) – Mass spectrum for recallibration

  • error_table (ErrorTable object) – Optional. If None - calculate for spec. ErrorTable object contain table error in ppm for mass, default 100 string

  • how ({'assign', 'mdm', filename}) – Optional. Default ‘assign’. If error_table is None we can choose how to recalculate. ‘assign’ - by assign error, default. ‘mdm’ - by calculation mass-difference map. filename - path to etalon spectrum, treated and saved by nomspectra

  • mode (str) – Optional. Default ‘-’ negative mode. May be +, - or 0

  • draw (bool) – Plot error (fit of KDM)

Return type

Spectrum