old_contents: """
  Two dimensional trace plot
  ===============
  """
  from msmbuilder.example_datasets import FsPeptide
  from msmbuilder.featurizer import DihedralFeaturizer
  from msmbuilder.decomposition import tICA
  from msmbuilder.cluster import MiniBatchKMeans
  from msmbuilder.msm import MarkovStateModel
  
  import numpy as np
  
  import msmexplorer as msme
  
  rs = np.random.RandomState(42)
  
  # Load Fs Peptide Data
  trajs = FsPeptide().get().trajectories
  
  # Extract Backbone Dihedrals
  featurizer = DihedralFeaturizer(types=['phi', 'psi'])
  diheds = featurizer.fit_transform(trajs)
  
  # Perform Dimensionality Reduction
  tica_model = tICA(lag_time=2, n_components=2)
  tica_trajs = tica_model.fit_transform(diheds)
  
  # Plot free 2D free energy (optional)
  txx = np.concatenate(tica_trajs, axis=0)
  ax = msme.plot_free_energy(
      txx, obs=(0, 1), n_samples=100000,
      random_state=rs,
      shade=True,
      clabel=True,
      clabel_kwargs={'fmt': '%.1f'},
      cbar=True,
      cbar_kwargs={'format': '%.1f', 'label': 'Free energy (kcal/mol)'}
  )
  # Now plot the first single trajectory on top of it to inspect it's movement
  msme.plot_trace2d(
      data=tica_trajs[0], ts=.2, ax=ax,
      scatter_kwargs={'s': 2},
      cbar_kwargs={'format': '%.1f', 'label': 'Time (ns)',
                   'orientation': 'horizontal'},
      xlabel='tIC 1', ylabel='tIC 2'
  )
  
new_contents: """
  Two dimensional trace plot
  ===============
  """
  from msmbuilder.example_datasets import FsPeptide
  from msmbuilder.featurizer import DihedralFeaturizer
  from msmbuilder.decomposition import tICA
  from msmbuilder.cluster import MiniBatchKMeans
  from msmbuilder.msm import MarkovStateModel
  from matplotlib import pyplot as pp
  import numpy as np
  
  import msmexplorer as msme
  
  rs = np.random.RandomState(42)
  
  # Load Fs Peptide Data
  trajs = FsPeptide().get().trajectories
  
  # Extract Backbone Dihedrals
  featurizer = DihedralFeaturizer(types=['phi', 'psi'])
  diheds = featurizer.fit_transform(trajs)
  
  # Perform Dimensionality Reduction
  tica_model = tICA(lag_time=2, n_components=2)
  tica_trajs = tica_model.fit_transform(diheds)
  
  # Plot free 2D free energy (optional)
  txx = np.concatenate(tica_trajs, axis=0)
  ax = msme.plot_free_energy(
      txx, obs=(0, 1), n_samples=100000,
      random_state=rs,
      shade=True,
      clabel=True,
      clabel_kwargs={'fmt': '%.1f'},
      cbar=True,
      cbar_kwargs={'format': '%.1f', 'label': 'Free energy (kcal/mol)'}
  )
  # Now plot the first single trajectory on top of it to inspect it's movement
  msme.plot_trace2d(
      data=tica_trajs[0], ts=.2, ax=ax,
      scatter_kwargs={'s': 2},
      cbar_kwargs={'format': '%.1f', 'label': 'Time (ns)',
                   'orientation': 'horizontal'},
      xlabel='tIC 1', ylabel='tIC 2'
  )
  
  # Finally, let's plot every trajectory to see the region that each one is covering
  f, ax = pp.subplots()
  msme.plot_trace2d(tica_trajs, ax)
  
subject: Add multi array example