import cobra from cobra.test import ecoli_pickle, create_test_model from cobra.flux_analysis.phenotype_phase_plane import calculate_phenotype_phase_plane model = create_test_model(ecoli_pickle) model # Output: # <Model iJO1366 at 0x5b0abd0> # We want to make a phenotype phase plane to evaluate uptakes of Glucose and # Oxygen. # # With [matplotlib](http://matplotlib.org) installed, this is as simple as data = calculate_phenotype_phase_plane(model, "EX_glc_e", "EX_o2_e") data.plot_matplotlib() # If [brewer2mpl](https://pypi.python.org/pypi/brewer2mpl/) is installed, other # color schemes can be used as well data.plot_matplotlib("Pastel1") data.plot_matplotlib("Dark2") # The number of points which are plotted in each dimension can also be changed calculate_phenotype_phase_plane( model, "EX_glc_e", "EX_o2_e", reaction1_npoints=20, reaction2_npoints=20 ).plot_matplotlib() # The code can also use multiple processes to speed up calculations
def PhasePlane(self, reac1, reac2, reac1_max=20, reac2_max=20, reac1_n=50, reac2_n=50, solver=None, n_processes=1, tol=1e-10): return phenotype_phase_plane.calculate_phenotype_phase_plane(self, reac1=reac1 ,reac2=reac2 , reac1_max=reac1_max, reac2_max=reac2_max, reac1_n=reac1_n, reac2_n=reac2_n, solver=solver, n_processes=n_processes, tol=tol)
from cobra.test import ecoli_pickle, create_test_model from cobra.flux_analysis.phenotype_phase_plane import \ calculate_phenotype_phase_plane model = create_test_model(ecoli_pickle) model # Output: # <Model iJO1366 at 0x5b0abd0> # We want to make a phenotype phase plane to evaluate uptakes of Glucose and # Oxygen. # # With [matplotlib](http://matplotlib.org) installed, this is as simple as data = calculate_phenotype_phase_plane(model, "EX_glc_e", "EX_o2_e") data.plot_matplotlib() # If [brewer2mpl](https://pypi.python.org/pypi/brewer2mpl/) is installed, other # color schemes can be used as well data.plot_matplotlib("Pastel1") data.plot_matplotlib("Dark2") # The number of points which are plotted in each dimension can also be changed calculate_phenotype_phase_plane(model, "EX_glc_e", "EX_o2_e", reaction1_npoints=20, reaction2_npoints=20).plot_matplotlib()
# #### | YOU CAN TOUCH AGAIN | # ### Phenotype Phase Plane # In[29]: from cobra.flux_analysis.phenotype_phase_plane import calculate_phenotype_phase_plane import matplotlib.pyplot as plt # In[ ]: get_ipython().magic(u'matplotlib inline') data = calculate_phenotype_phase_plane(model, "PEPCARBOX_RXN_c_phase1", "Starch_link1_2") data.plot_matplotlib(); # # Constraints Scan # In[1]: model.ConstraintScan({"Citrate_link1_2": 1}, 0, 100, 101) # In[ ]: