Skip to content

Commit

Permalink
Pass grid kwarg to spectrum_utils
Browse files Browse the repository at this point in the history
  • Loading branch information
@levitsky
levitsky committed Jan 30, 2025
1 parent f506367 commit 24a2037
Show file tree
Hide file tree
Showing 2 changed files with 36 additions and 28 deletions.
62 changes: 35 additions & 27 deletions pyteomics/pylab_aux.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -160,8 +160,8 @@ def scatter_trend(x, y=None, **kwargs):
pylab.ylabel(kwargs.get('ylabel', ''))

equation = (
'$y\,=\,{:.3f}x\,{}\,{:.3f}$, '
'$R^2=\,{:.3f}$ \n$\sigma\,=\,{:.3f}$'.format(
r'$y\,=\,{:.3f}x\,{}\,{:.3f}$, '
r'$R^2=\,{:.3f}$ \n$\sigma\,=\,{:.3f}$'.format(
a, '-' if b < 0 else '+', abs(b), r*r, stderr))

if y is None:
Expand Down Expand Up @@ -246,23 +246,20 @@ def plot_function_3d(x, y, function, **kwargs):
plot_type = kwargs.pop('plot_type', 'surface')
if plot_type == 'surface':
ax.plot_surface(X, Y, Z,
rstride=kwargs.pop('rstride', 1),
cstride=kwargs.pop('cstride', 1),
cmap=kwargs.pop('cmap', pylab.cm.jet),
**kwargs)
rstride=kwargs.pop('rstride', 1),
cstride=kwargs.pop('cstride', 1),
cmap=kwargs.pop('cmap', pylab.cm.jet),
**kwargs)
elif plot_type == 'wireframe':
ax.plot_wireframe(X, Y, Z,
cmap=kwargs.pop('cmap', pylab.cm.jet), **kwargs)
ax.plot_wireframe(X, Y, Z, cmap=kwargs.pop('cmap', pylab.cm.jet), **kwargs)
elif plot_type == 'scatter':
ax.scatter3D(np.ravel(X), np.ravel(Y), np.ravel(Z), **kwargs)
elif plot_type == 'contour':
num_contours = kwargs.pop('num_contours', 50)
ax.contour3D(X, Y, Z, num_contours,
cmap=kwargs.pop('cmap', pylab.cm.jet), **kwargs)
ax.contour3D(X, Y, Z, num_contours, cmap=kwargs.pop('cmap', pylab.cm.jet), **kwargs)
elif plot_type == 'contourf':
num_contours = kwargs.pop('num_contours', 50)
ax.contourf3D(X, Y, Z, num_contours,
cmap=kwargs.pop('cmap', pylab.cm.jet), **kwargs)
ax.contourf3D(X, Y, Z, num_contours, cmap=kwargs.pop('cmap', pylab.cm.jet), **kwargs)
else:
raise PyteomicsError('Unknown plot type: {}'.format(plot_type))

Expand Down Expand Up @@ -299,11 +296,10 @@ def plot_function_contour(x, y, function, **kwargs):
Z = np.array(Z)
num_contours = kwargs.pop('num_contours', 50)
if kwargs.pop('filling', True):
pylab.contourf(X, Y, Z, num_contours,
cmap=kwargs.pop('cmap', pylab.cm.jet), **kwargs)
plot_func = pylab.contourf
else:
pylab.contour(X, Y, Z, num_contours,
cmap=kwargs.pop('cmap', pylab.cm.jet), **kwargs)
plot_func = pylab.contour
plot_func(X, Y, Z, num_contours, cmap=kwargs.pop('cmap', pylab.cm.jet), **kwargs)


def plot_qvalue_curve(qvalues, *args, **kwargs):
Expand Down Expand Up @@ -484,13 +480,15 @@ def _default_annotate_spectrum(spectrum, peptide, *args, **kwargs):
for charge in range(1, maxcharge + 1):
if ion[0] in 'abc':
for i in range(2, n):
mz.setdefault(ion, []).append(mass.fast_mass2(parsed[:i] + [parser.std_cterm],
aa_mass=aa_mass, charge=charge, ion_type=ion, mass_data=mass_data, ion_comp=ion_comp))
mz.setdefault(ion, []).append(
mass.fast_mass2(parsed[:i] + [parser.std_cterm], aa_mass=aa_mass, charge=charge,
ion_type=ion, mass_data=mass_data, ion_comp=ion_comp))
names.setdefault(ion, []).append(ion[0] + str(i - 1) + ion[1:])
else:
for i in range(1, n - 1):
mz.setdefault(ion, []).append(mass.fast_mass2([parser.std_nterm] + parsed[n - (i + 1):],
aa_mass=aa_mass, charge=charge, ion_type=ion, mass_data=mass_data, ion_comp=ion_comp))
mz.setdefault(ion, []).append(
mass.fast_mass2([parser.std_nterm] + parsed[n - (i + 1):], aa_mass=aa_mass, charge=charge,
ion_type=ion, mass_data=mass_data, ion_comp=ion_comp))
names.setdefault(ion, []).append(ion[0] + str(i) + ion[1:])
texts = []
for ion in types:
Expand Down Expand Up @@ -558,7 +556,8 @@ def _spectrum_utils_create_spectrum(spectrum, *args, **kwargs):
if mz_range:
spectrum = spectrum.set_mz_range(*mz_range)

spectrum = spectrum.filter_intensity(min_intensity=min_intensity, max_num_peaks=max_num_peaks
spectrum = spectrum.filter_intensity(
min_intensity=min_intensity, max_num_peaks=max_num_peaks
).scale_intensity(scaling, max_intensity)
return spectrum

Expand All @@ -581,7 +580,8 @@ def _spectrum_utils_annotate_spectrum(spectrum, peptide, *args, **kwargs):
if precursor_charge is None:
precursor_charge = _get_precursor_charge(spectrum)
if precursor_charge is None:
raise PyteomicsError('Could not extract precursor charge from spectrum. '
raise PyteomicsError(
'Could not extract precursor charge from spectrum. '
'Please specify `precursor_charge` keyword argument.')

maxcharge = kwargs.pop('maxcharge', max(1, precursor_charge - 1))
Expand Down Expand Up @@ -646,16 +646,18 @@ def _spectrum_utils_annotate_plot(spectrum, peptide, *args, **kwargs):

with SpectrumUtilsColorScheme(kwargs.pop('colors', None)):
spectrum = _spectrum_utils_annotate_spectrum(spectrum, peptide, *args, **kwargs)
return spectrum, sup.spectrum(spectrum, annot_kws=kwargs.pop('text_kw', None), ax=kwargs.pop('ax', None),
annot_fmt=kwargs.pop('annot_fmt', str))
return spectrum, sup.spectrum(
spectrum, annot_kws=kwargs.pop('text_kw', None), ax=kwargs.pop('ax', None),
annot_fmt=kwargs.pop('annot_fmt', str), grid=kwargs.pop('grid', True))


def _spectrum_utils_annotate_iplot(spectrum, peptide, *args, **kwargs):
import spectrum_utils.iplot as supi
with SpectrumUtilsColorScheme(kwargs.pop('colors', None)):
spectrum = _spectrum_utils_annotate_spectrum(spectrum, peptide, *args, **kwargs)
return spectrum, supi.spectrum(spectrum, annot_kws=kwargs.pop('text_kw', None),
annot_fmt=kwargs.pop('annot_fmt', str))
return spectrum, supi.spectrum(
spectrum, annot_kws=kwargs.pop('text_kw', None),
annot_fmt=kwargs.pop('annot_fmt', str), grid=kwargs.pop('grid', True))


_annotation_backends = {
Expand Down Expand Up @@ -724,7 +726,7 @@ def annotate_spectrum(spectrum, peptide, *args, **kwargs):
remove_precursor_peak : bool, keyword only, optional
Remove precursor peak from spectrum before annotation. Default is :py:const:`False`.
Only works with `spectrum_utils` backend.
Only works with `spectrum_utils` and `spectrum_utils.iplot` backends.
min_intensity : float, keyword only, optional
Remove low-intensity peaks; this is a factor of maximum peak intensity. Default is 0 (no filtering).
Only works with `spectrum_utils` and `spectrum_utils.iplot` backends.
Expand All @@ -738,6 +740,12 @@ def annotate_spectrum(spectrum, peptide, *args, **kwargs):
(the default is :py:const:`None`, which means that no scaling
relative to the most intense peak will be performed).
Only works with `spectrum_utils` and `spectrum_utils.iplot` backends.
annot_fmt : callable, keyword-only, optional
Passed to :py:func:`spectrum_utils.plot.spectrum`.
Only works with `spectrum_utils` and `spectrum_utils.iplot` backends.
grid : bool, keyword-only, optional
Passed to :py:func:`spectrum_utils.plot.spectrum`. Default is :py:const:`True`.
Only works with `spectrum_utils` and `spectrum_utils.iplot` backends.
aa_comp : dict, keyword only, optional
Amino acid compositions, including modified ones. If given, will be used for conversion from *modX* to ProForma.
mod_names : dict or callable, keyword only, optional
Expand Down
2 changes: 1 addition & 1 deletion pyteomics/version.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@
"""

__version__ = '4.7.5'
__version__ = '4.7.6a1'

from collections import namedtuple
import re
Expand Down

0 comments on commit 24a2037

Please sign in to comment.