matchms.plotting package

Functions for plotting one or multiple spectra

Matchms provides (limited) plotting functionality to display one or multiple spectra from Spectrum objects.

Currently this includes 3 different plot types:

  • plot_spectrum(spectrum) or spectrum.plot() This will create a plot of an individual spectrum.

  • plot_spectra_mirror(spectrum1, spectrum2) or spectrum1.plot_against(spectrum2) This will create a mirro plot comparing two spectra.

  • plot_spectra_array([spec1, spec2, …]) This will create a plot with an array of all spectra in the given list.

Example of how to visually compare two spectra:

import os
from matplotlib import pyplot as plt
import matchms.filtering as msfilters
from matchms.importing import load_from_msp

module_root = os.getcwd()
spectrums_file = os.path.join(module_root, "matchms", "tests", "MoNA-export-GC-MS-first10.msp")
spectrums = list(load_from_msp(spectrums_file))
spectrums = [msfilters.default_filters(s) for s in spectrums]

spectrums[1].plot()
# plt.savefig("spectrum-plot-example_1.png", dpi=300)  # If you want to save a plot
matchms spectrum plot

Plot of individual spectrum.

Another example is to compare two spectra visually using a mirror plot:

spectrums[2].plot_against(spectrums[3])
plt.xlim(0, 200)
matchms spectrum mirror plot

Compare two spectra visually using a mirror plot.

Finally, it is also possible to plot many spectra at once using plot_spectra_array():

from matchms.plotting import plot_spectra_array
plot_spectra_array(spectrums[:4])
matchms spectra array plot

Compare many spectra visually using an array plot.

matchms.plotting.plot_spectra_array(spectrums, n_cols: int = 2, peak_color='darkblue', dpi: int = 200, **spectrum_kws) → matplotlib.axes._axes.Axes[source]

Mirror plot two MS/MS spectra.

Code is largely taken from package “spectrum_utils”.

Parameters

  • spectrums (list of matchms.Spectrum) – List of spectra to be plotted in a single figure.

  • n_cols – Number of spectra to be plotted per row. Default is 4.

  • spectrum_kws – Keyword arguments for plot_spectrum().

matchms.plotting.plot_spectra_mirror(spec_top, spec_bottom, ax: Optional[matplotlib.axes._axes.Axes] = None, **spectrum_kws) → matplotlib.axes._axes.Axes[source]

Mirror plot two MS/MS spectra.

Code is largely taken from package “spectrum_utils”.

Parameters

  • spec_top (matchms.Spectrum) – The spectrum to be plotted on the top.

  • spec_bottom (matchms.Spectrum) – The spectrum to be plotted on the bottom.

  • ax – Axes instance on which to plot the spectrum. If None the current Axes instance is used.

  • spectrum_kws – Keyword arguments for plot_spectrum().

Returns

The matplotlib Axes instance on which the spectra are plotted.

Return type

plt.Axes

matchms.plotting.plot_spectrum(spectrum, annotate_ions: bool = False, mirror_intensity: bool = False, grid: Union[bool, str] = True, ax: Optional[matplotlib.axes._axes.Axes] = None, peak_color='teal', **plt_kwargs) → matplotlib.axes._axes.Axes[source]

Plot a single MS/MS spectrum.

Code is largely taken from package “spectrum_utils”.

Parameters

  • spectrum (matchms.Spectrum) – The spectrum to be plotted.

  • annotate_ions – Flag indicating whether or not to annotate fragment using peak comments (if present in the spectrum). The default is True.

  • mirror_intensity – Flag indicating whether to flip the intensity axis or not.

  • grid – Draw grid lines or not. Either a boolean to enable/disable both major and minor grid lines or ‘major’/’minor’ to enable major or minor grid lines respectively.

  • ax – Axes instance on which to plot the spectrum. If None the current Axes instance is used.

Returns

The matplotlib Axes instance on which the spectrum is plotted.

Return type

plt.Axes

Submodules