diff --git a/docs/source/user_guide/spectrum_merging.rst b/docs/source/user_guide/spectrum_merging.rst index 5a429399e..c82176d7d 100644 --- a/docs/source/user_guide/spectrum_merging.rst +++ b/docs/source/user_guide/spectrum_merging.rst @@ -106,11 +106,11 @@ The block size could be adjusted by using ``block_method:rt_block_size`` paramet # again load MS data and store as MSExperiment object exp = oms.MSExperiment() - oms.MzMLFile().load('test.mzML', exp) + oms.MzMLFile().load("test.mzML", exp) # again load MS data and store as MSExperiment object exp = oms.MSExperiment() - oms.MzMLFile().load('test.mzML', exp) + oms.MzMLFile().load("test.mzML", exp) # adjust block size to 10 spectra and merge merger = oms.SpectraMerger() @@ -136,9 +136,9 @@ The block size could be adjusted by using ``block_method:rt_block_size`` paramet axs[i].set_ylim(1e3, 1e7) axs[i].set_xlim(360, 1000) axs[i].title.set_text( - "Merged MS1 spectrum with 10 scans' + "Merged MS1 spectrum with 10 scans" if i == 0 - else 'Merged MS1 spectrum with 5 scans" + else "Merged MS1 spectrum with 5 scans" ) plt.show() @@ -170,13 +170,13 @@ Next we perform MS2 spectra merging with precursor method by using the ``mergeSp # load MS data and store as MSExperiment object exp = oms.MSExperiment() - oms.MzMLFile().load('test.mzML', exp) + oms.MzMLFile().load("test.mzML", exp) spectra = exp.getSpectra() # spectra with ms_level = 2 spectra_ms2 = [s for s in spectra if s.getMSLevel() == 2] - print(f'Number of MS2 spectra before merge are {len(spectra_ms2)}') + print(f"Number of MS2 spectra before merge are {len(spectra_ms2)}") # merge spectra with similar precursors merger = oms.SpectraMerger() @@ -184,7 +184,7 @@ Next we perform MS2 spectra merging with precursor method by using the ``mergeSp spectraMerged = exp.getSpectra() spectraMerged_ms2 = [s for s in spectraMerged if s.getMSLevel() == 2] - print(f'Number of MS2 spectra after merge are {len(spectraMerged_ms2)}') + print(f"Number of MS2 spectra after merge are {len(spectraMerged_ms2)}") .. code-block:: output @@ -304,12 +304,12 @@ On the other hand, the ``tophat`` method, as the name implies, performs a simple # load MS data and store as MSExperiment object exp = oms.MSExperiment() - oms.MzMLFile().load('test.mzML', exp) + oms.MzMLFile().load("test.mzML", exp) spectra = exp.getSpectra() # number of MS1 spectra before averaging spectra_ms1 = [s for s in spectra if s.getMSLevel() == 1] - print(f'Number of MS1 spectra before averaging are {len(spectra_ms1)}') + print(f"Number of MS1 spectra before averaging are {len(spectra_ms1)}") # average spectra with gaussian merger = oms.SpectraMerger() @@ -318,7 +318,7 @@ On the other hand, the ``tophat`` method, as the name implies, performs a simple # number of MS1 spectra after averaging spectraAveraged_ms1 = [s for s in spectraAveraged if s.getMSLevel() == 1] - print(f'Number of MS1 spectra after averaging are {len(spectraAveraged_ms1)}') + print(f"Number of MS1 spectra after averaging are {len(spectraAveraged_ms1)}") fig, axs = plt.subplots(2) fig.set_figheight(4) @@ -330,7 +330,7 @@ On the other hand, the ``tophat`` method, as the name implies, performs a simple axs[i].set_yscale("log") axs[i].set_ylim(5e2, 1e6) axs[i].set_xlim(360, 600) - axs[i].title.set_text('Before averaging' if i == 0 else 'After averaging') + axs[i].title.set_text("Before averaging" if i == 0 else "After averaging") plt.show() # store modified data