Butterfly Plot

[BenSamy2020]

Butterfly Plot

[bittremieux]

Hi Ben, indeed, the annotate_peptide_fragments function and subsequent plotting will color fragments that match the theoretical fragments of the peptide. If I understand your question correctly, instead you want to highlight peaks that match between both spectra? That isn't directly supported, but you should still be able to do it with some "hacking".

To highlight matching peaks you first need to determine those peaks. You could do that like this:

fragment_mz_tolerance = 0.05
peak_matches = []
j = 0
for i in range(len(spectrum1.mz)):
    while j < len(spectrum2.mz) and spectrum2.mz[j] + fragment_mz_tolerance < spectrum1.mz[i]:
        j += 1
    if abs(spectrum1.mz[i] - spectrum2.mz[j]) < fragment_mz_tolerance:
        peak_matches.append((i, j))

Next, you need to annotate the matching peaks:

import spectrum_utils.spectrum as sus

spectrum1.annotation = np.full_like(spectrum1.mz, None, object)
spectrum2.annotation = np.full_like(spectrum2.mz, None, object)
for i, j in peak_matches:
    fragment_annotation = sus.PeptideFragmentAnnotation(1, spectrum1.mz[i], 'z', 0)
    fragment_annotation.ion_type = 'match'
    spectrum1.annotation[peak_match[0]] = spectrum2.annotation[peak_match[1]] = \
        fragment_annotation

Finally, choose a color for the matching peaks and plot the spectra:

import spectrum_utils.plot as sup

sup.colors['match'] = 'red'

fig, ax = plt.subplots(figsize=(12, 6))
sup.mirror(spectrum1, spectrum2, {'color_ions': True, 'annotate_ions': False}, ax=ax)
plt.show()
plt.close()

Please let me know if this works for you.

Note: I just wrote the code snippets here without testing them, so maybe some minor fixes are needed to actually run it.

[BenSamy2020]

Greetings,

Sorry for the late response. Your suggestions works!