unidec.LipiDec package

Subpackages

• unidec.LipiDec.Infusion package
  • Submodules
  • unidec.LipiDec.Infusion.Formulas module
    • get_count()
  • unidec.LipiDec.Infusion.LipiDecEng module
    • LipiDec
      • LipiDec.apply_ratio()
      • LipiDec.cleanup_db()
      • LipiDec.correct_peaks()
      • LipiDec.detect_coalescence()
      • LipiDec.find_alternates()
      • LipiDec.find_good_species()
      • LipiDec.find_initial_matches()
      • LipiDec.find_isotope_matches()
      • LipiDec.find_matches()
      • LipiDec.find_missing_peaks()
      • LipiDec.get_peaks()
      • LipiDec.make_spectrum()
      • LipiDec.plot_hits()
      • LipiDec.run_decon()
      • LipiDec.sort_df()
    • LipiDecRunner
      • LipiDecRunner.make_plot()
      • LipiDecRunner.run()
    • matcher()
  • unidec.LipiDec.Infusion.LipiDec_DataBaseGenerator module
    • adduct_mass()
    • construct_mol()
    • find_basemods()
    • get_subs()
    • make_adduct_db()
    • make_subs_list()
    • massfromsmiles()
    • massfromstruct()
    • sum_comp_only()
  • unidec.LipiDec.Infusion.ShotgunLipiDec module
  • unidec.LipiDec.Infusion.ShotgunLipiDecMTM module
  • Module contents

Submodules

unidec.LipiDec.AddFeaturestoDF module

unidec.LipiDec.AddFeaturestoDF.calc_tail_diff(df, class_col='Class Name', tail_col='Tail Lengths', unsat_col='Tail Unsaturation', weight_col=None)

unidec.LipiDec.AddFeaturestoDF.clean_name(name)

unidec.LipiDec.AddFeaturestoDF.fill_out_df(df)

unidec.LipiDec.AddFeaturestoDF.fill_out_df_names(df, name='Metabolite name')

unidec.LipiDec.AddFeaturestoDF.get_class(name)

unidec.LipiDec.AddFeaturestoDF.get_colors(unique_classes)

unidec.LipiDec.AddFeaturestoDF.get_internal_standards(classname, classes)

unidec.LipiDec.AddFeaturestoDF.get_overall_tails(name)

unidec.LipiDec.AddFeaturestoDF.get_symbols(unique_classes)

unidec.LipiDec.AddFeaturestoDF.isotope_ratios(df)

unidec.LipiDec.AddFeaturestoDF.kendrick_analysis(mz, charge)

unidec.LipiDec.AddFeaturestoDF.mass_defect_df(df, ref_col='Reference m/z', ex_col='Average Mz', z_col='Charge')

unidec.LipiDec.AddFeaturestoDF.parse_names(df, namecolumn='Metabolite name', parse_adduct=True)

unidec.LipiDec.AddFeaturestoDF.set_class_name(df, name='Metabolite name')

unidec.LipiDec.AddFeaturestoDF.set_tails(df, name='Metabolite name')

unidec.LipiDec.LipyDec module

class unidec.LipiDec.LipyDec.LipDropTarget(window)

Bases: FileDropTarget

OnDropFiles(x, y, filenames)

When files are dropped, either open a single file or run in batch.

class unidec.LipiDec.LipyDec.LipyDecWindow(parent, engine=None)

Bases: Frame

check_only(e=0)

check_only2(e=0)

check_only3(e=0)

color_class_checkbox(e=0, white=False)

color_length_checkbox(e=0, white=False)

color_unsat_checkbox(e=0, white=False)

find_active_plot()

find_mouse_species(xpos, ypos)

fold_plot(e=0)

load_check2(e=0, force_refresh=False)

load_check3(e=0, force_refresh=False)

load_checkboxes()

make_plot_4(e=0)

fold = self.df2[“FoldChange”+self.normname].to_numpy() avga = self.df2[“AvgA_0”].to_numpy() self.plot4.scatterplottop(avga, fold, color = self.colors)

make_plot_5(e=0)

make_plots()

md_plot(e=0)

on_close(e)

Close the window. :param e: Unused event :return: None

on_motion(xpos, ypos)

on_open(e=None)

on_open_file(path)

on_save_fig(e)

Saves the figures in self.directory as PNGs. :param e: Unused event :return: None

on_save_fig_pdf(e)

Saves the figures in self.directory as PDFs. :param e: Unused event :return: None

process_df()

rt_plot(e=0)

update_check2(e=0)

update_check3(e=0)

update_checks(e=0, force_refresh2=False, force_refresh3=False)

unidec.LipiDec.SkyQuant module

unidec.LipiDec.SkyQuant.calc_fold_changes_all(df, g1=1, g0=0, n0=3, n1=3)

unidec.LipiDec.SkyQuant.filter_skyline(df)

unidec.LipiDec.SkyQuant.find_file_headers(df)

unidec.LipiDec.SkyQuant.find_std_class(df)

unidec.LipiDec.SkyQuant.full_processing(df)

unidec.LipiDec.SkyQuant.int_filter(df, threshold, norm='N3', g1=1, g0=0)

unidec.LipiDec.SkyQuant.norm_to_std(df, col_name)

unidec.LipiDec.SkyQuant.rel_quant(df, ngroups, nreps)

unidec.LipiDec.SkyQuant.sd_filter(df, threshold)

unidec.LipiDec.SkyQuant.set_avg_rt_mz(df)

unidec.LipiDec.SkyQuant.set_avg_std(df, areas, i, name='')

unidec.LipiDec.SkyQuant.set_colors(df)

unidec.LipiDec.SkyQuant.set_stds(df)

unidec.LipiDec.SkyQuant.translate(df)

Module contents