def showCrossProjection(ensemble, mode_x, mode_y, scale=None, scalar=None,
*args, **kwargs):
"""Show a projection of conformational deviations onto modes from
different models using :func:`~matplotlib.pyplot.plot`. This function
differs from :func:`showProjection` by accepting modes from two different
models.
:arg ensemble: Ensemble for which deviations will be projected
:type ensemble: :class:`~prody.ensemble.Ensemble`
:arg mode_x: Projection onto this mode will be shown along x-axis.
:type mode_x: :class:`Mode`
:arg mode_y: Projection onto this mode will be shown along y-axis.
:type mode_y: :class:`Mode`
:arg scale: Scale width of the projection onto one of modes.
``x`` and ``y`` are accepted.
:type scale: str
:arg scalar: Scalar factor for ``x`` or ``y``. If ``scalar=None`` is
passed, best scaling factor will be calculated and printed on the
console.
:type scalar: float
The projected values are by default converted to RMSD.
Pass ``rmsd=False`` to calculate raw projection values.
:class:`Vector` instances are accepted as *ensemble* argument to allow
for projecting a deformation vector onto normal modes.
By default ``marker='o', ls='None'`` is passed to the plotting function
to disable lines.
.. plot::
:context:
:include-source:
plt.figure(figsize=(5.2,4))
showCrossProjection(p38_ensemble, p38_pca[0], p38_anm[2])
.. plot::
:context:
:nofigs:
plt.close('all')
|example| See :ref:`pca-xray-plotting` for a more elaborate example."""
import matplotlib.pyplot as plt
if not isinstance(ensemble, (Ensemble, Conformation, Vector)):
raise TypeError('ensemble must be Ensemble, Conformation, or Vector, '
'not {0:s}'.format(type(ensemble)))
if not isinstance(mode_x, VectorBase):
raise TypeError('mode_x must be a Mode instance, not {0:s}'
.format(type(mode_x)))
if not mode_x.is3d():
raise ValueError('mode_x must be 3-dimensional')
if not isinstance(mode_y, VectorBase):
raise TypeError('mode_y must be a Mode instance, not {0:s}'
.format(type(mode_y)))
if not mode_y.is3d():
raise ValueError('mode_y must be 3-dimensional')
if scale is not None:
assert isinstance(scale, str), 'scale must be a string'
scale = scale.lower()
assert scale in ('x', 'y'), 'scale must be x or y'
if scalar is not None:
assert isinstance(scalar, float), 'scalar must be a float'
xcoords = calcProjection(ensemble, mode_x, kwargs.get('rmsd', True))
ycoords = calcProjection(ensemble, mode_y, kwargs.pop('rmsd', True))
if scale:
if scalar is None:
scalar = ((ycoords.max() - ycoords.min()) /
(xcoords.max() - xcoords.min()))
scalar = scalar * np.sign(calcOverlap(mode_x, mode_y))
if scale == 'x':
LOGGER.info('Projection onto {0:s} is scaled by {1:.2f}'
.format(mode_x, scalar))
else:
scalar = 1 / scalar
LOGGER.info('Projection onto {0:s} is scaled by {1:.2f}'
.format(mode_y, scalar))
if scale == 'x':
xcoords = xcoords * scalar
else:
ycoords = ycoords * scalar
if 'ls' not in kwargs:
kwargs['ls'] = 'None'
if 'marker' not in kwargs:
kwargs['marker'] = 'o'
show = plt.plot(xcoords, ycoords, *args, **kwargs)
plt.xlabel('{0:s} coordinate'.format(mode_x))
plt.ylabel('{0:s} coordinate'.format(mode_y))
return show
def showProjection(ensemble, modes, *args, **kwargs):
"""Show a projection of conformational deviations onto up to three normal
modes from the same model.
:arg ensemble: an ensemble, trajectory or a conformation for which
deviation(s) will be projected, or a deformation vector
:type ensemble: :class:`~.Ensemble`, :class:`~.Conformation`,
:class:`~.Vector`, :class:`~.Trajectory`
:arg modes: up to three normal modes
:type modes: :class:`~.Mode`, :class:`~.ModeSet`, :class:`~.NMA`
:arg color: a color name or a list of color name, default is ``'blue'``
:type color: str, list
:arg label: label or a list of labels
:type label: str, list
:arg marker: a marker or a list of markers, default is ``'o'``
:type marker: str, list
:arg linestyle: line style, default is ``'None'``
:type linestyle: str
:arg text: list of text labels, one for each conformation
:type text: list
:arg fontsize: font size for text labels
:type fontsize: int
The projected values are by default converted to RMSD. Pass ``rmsd=False``
to use projection itself.
Matplotlib function used for plotting depends on the number of modes:
* 1 mode: :func:`~matplotlib.pyplot.hist`
* 2 modes: :func:`~matplotlib.pyplot.plot`
* 3 modes: :meth:`~mpl_toolkits.mplot3d.Axes3D.plot`
.. plot::
:context:
:include-source:
plt.figure(figsize=(5,4))
showProjection(p38_ensemble, p38_pca[0])
plt.title('Projection onto PC1')
plt.figure(figsize=(5,4))
showProjection(p38_ensemble, p38_pca[:2])
plt.title('Projection onto PC1-2')
plt.figure(figsize=(5,4))
showProjection(p38_ensemble, p38_pca[:3]) # onto top 3 PCs
plt.title('Projection onto PC1-3')
.. plot::
:context:
:nofigs:
plt.close('all')"""
import matplotlib.pyplot as plt
projection = calcProjection(ensemble, modes, kwargs.pop('rmsd', True))
if projection.ndim == 1 or projection.shape[1] == 1:
show = plt.hist(projection.flatten(), *args, **kwargs)
plt.xlabel('{0:s} coordinate'.format(str(modes)))
plt.ylabel('Number of conformations')
return show
elif projection.shape[1] > 3:
raise ValueError('Projection onto up to 3 modes can be shown. '
'You have given {0:d} mode.'.format(len(modes)))
num = projection.shape[0]
markers = kwargs.pop('marker', 'o')
if isinstance(markers, str) or markers is None:
markers = [markers] * num
elif isinstance(markers, list):
if len(markers) != num:
raise ValueError('length of marker must be {0:d}'.format(num))
else:
raise TypeError('marker must be a string or a list')
colors = kwargs.pop('color', 'blue')
if isinstance(colors, str) or colors is None:
colors = [colors] * num
elif isinstance(colors, list):
if len(colors) != num:
raise ValueError('length of color must be {0:d}'.format(num))
else:
raise TypeError('color must be a string or a list')
labels = kwargs.pop('label', None)
if isinstance(labels, str) or labels is None:
labels = [labels] * num
elif isinstance(labels, list):
if len(labels) != num:
raise ValueError('length of label must be {0:d}'.format(num))
elif labels is not None:
raise TypeError('label must be a string or a list')
kwargs['ls'] = kwargs.pop('linestyle', None) or kwargs.pop('ls', 'None')
texts = kwargs.pop('text', None)
if texts:
if not isinstance(texts, list):
raise TypeError('text must be a list')
elif len(texts) != num:
raise TypeError('length of text must be {0:d}'.format(num))
size = kwargs.pop('fontsize', None) or kwargs.pop('size', None)
modes = [m for m in modes]
if len(modes) == 2:
plot = plt.plot
show = plt.gcf()
text = plt.text
else:
from mpl_toolkits.mplot3d import Axes3D
cf = plt.gcf()
show = None
for child in cf.get_children():
if isinstance(child, Axes3D):
show = child
break
if show is None:
show = Axes3D(cf)
plot = show.plot
text = show.text
indict = defaultdict(list)
for i, opts in enumerate(zip(markers, colors, labels)):
indict[opts].append(i)
args = list(args)
for opts, indices in indict.iteritems():
marker, color, label = opts
kwargs['marker'] = marker
kwargs['color'] = color
if label:
kwargs['label'] = label
else:
kwargs.pop('label', None)
plot(*(list(projection[indices].T) + args), **kwargs)
if texts:
kwargs = {}
if size:
kwargs['size'] = size
for args in zip(*(list(projection.T) + [texts])):
text(*args, **kwargs)
if len(modes) == 2:
plt.xlabel('{0:d} coordinate'.format(int(modes[0])+1))
plt.ylabel('{0:d} coordinate'.format(int(modes[1])+1))
elif len(modes) == 3:
show.set_xlabel('Mode {0:d} coordinate'.format(int(modes[0])+1))
show.set_ylabel('Mode {0:d} coordinate'.format(int(modes[1])+1))
show.set_zlabel('Mode {0:d} coordinate'.format(int(modes[2])+1))
return show
def showProjection(ensemble, modes, *args, **kwargs):
"""Show a projection of conformational deviations onto up to three normal
modes from the same model.
:arg ensemble: a :class:`~prody.ensemble.Ensemble` instance
:arg modes: a :class:`Mode`, :class:`ModeSet`, or :class:`NMA` instance
The projected values are by default converted to RMSD. Pass
``rmsd=False`` to use projection itself. :class:`Vector` instances
are accepted as *ensemble* argument to allow for projecting a
deformation vector onto normal modes.
Matplotlib function used for plotting depends on the number of modes:
* 1 mode: :func:`~matplotlib.pyplot.hist`
* 2 modes: :func:`~matplotlib.pyplot.plot`
* 3 modes: :meth:`mpl_toolkits.mplot3d.Axes3D.plot`
By default ``marker='o', ls='None'`` is passed to the plotting function
to disable lines in projections onto 2 or 3-d spaces.
.. plot::
:context:
:include-source:
plt.figure(figsize=(5,4))
showProjection(p38_ensemble, p38_pca[0])
plt.title('Projection onto PC1')
plt.figure(figsize=(5,4))
showProjection(p38_ensemble, p38_pca[:2])
plt.title('Projection onto PC1-2')
plt.figure(figsize=(5,4))
showProjection(p38_ensemble, p38_pca[:3]) # onto top 3 PCs
plt.title('Projection onto PC1-3')
.. plot::
:context:
:nofigs:
plt.close('all')"""
import matplotlib.pyplot as plt
if not isinstance(ensemble, (Ensemble, Conformation, Vector)):
raise TypeError('ensemble must be Ensemble, Conformation, or Vector, '
'not {0:s}'.format(type(ensemble)))
if not isinstance(modes, (NMA, ModeSet, Mode)):
raise TypeError('modes must be NMA, ModeSet, or Mode, not {0:s}'
.format(type(modes)))
if not modes.is3d():
raise Exception('modes must be 3-dimensional')
if isinstance(modes, Mode) or (isinstance(modes, (ModeSet, NMA)) and
len(modes)==1):
if not isinstance(modes, Mode):
modes = modes[0]
projection = calcProjection(ensemble, modes, kwargs.pop('rmsd', True))
show = plt.hist(projection.flatten(), *args, **kwargs)
plt.xlabel('Mode {0:d} coordinate'.format(modes.getIndex()+1))
plt.ylabel('Number of conformations')
elif len(modes) == 2:
if 'ls' not in kwargs:
kwargs['ls'] = 'None'
if 'marker' not in kwargs:
kwargs['marker'] = 'o'
projection = calcProjection(ensemble, modes, kwargs.pop('rmsd', True))
show = plt.plot(projection[:, 0], projection[:, 1], *args, **kwargs)
modes = [m for m in modes]
plt.xlabel('Mode {0:d} coordinate'.format(modes[0].getIndex()+1))
plt.ylabel('Mode {0:d} coordinate'.format(modes[1].getIndex()+1))
elif len(modes) == 3:
if 'ls' not in kwargs:
kwargs['ls'] = 'None'
if 'marker' not in kwargs:
kwargs['marker'] = 'o'
from mpl_toolkits.mplot3d import Axes3D
projection = calcProjection(ensemble, modes, kwargs.pop('rmsd', True))
modes = [m for m in modes]
cf = plt.gcf()
show = None
for child in cf.get_children():
if isinstance(child, Axes3D):
show = child
break
if show is None:
show = Axes3D(cf)
show.plot(projection[:, 0], projection[:, 1], projection[:, 2],
*args, **kwargs)
show.set_xlabel('Mode {0:d} coordinate'.format(modes[0].getIndex()+1))
show.set_ylabel('Mode {0:d} coordinate'.format(modes[1].getIndex()+1))
show.set_zlabel('Mode {0:d} coordinate'.format(modes[2].getIndex()+1))
else:
raise ValueError('Projection onto upto 3 modes can be shown. '
'You have given {0:d} mode.'.format(len(modes)))
return show