Phenotype Phase Plane

Phenotype phase planes will show distinct phases of optimal growth with different use of two different substrates. For more information, see Edwards et al.

Cobrapy supports calculating and plotting (using matplotlib) these phenotype phase planes. Here, we will make one for the "textbook" E. coli core model.



In [1]:

    
%matplotlib inline
from time import time


import cobra.test
from cobra.flux_analysis import calculate_phenotype_phase_plane

model = cobra.test.create_test_model("textbook")

We want to make a phenotype phase plane to evaluate uptakes of Glucose and Oxygen.



In [2]:

    
data = calculate_phenotype_phase_plane(model, "EX_glc__D_e", "EX_o2_e")
data.plot_matplotlib();

If brewer2mpl is installed, other color schemes can be used as well



In [3]:

    
data.plot_matplotlib("Pastel1")
data.plot_matplotlib("Dark2");

The number of points which are plotted in each dimension can also be changed



In [4]:

    
calculate_phenotype_phase_plane(model, "EX_glc__D_e", "EX_o2_e",
                                reaction1_npoints=20,
                                reaction2_npoints=20).plot_matplotlib();

The code can also use multiple processes to speed up calculations



In [5]:

    
start_time = time()
calculate_phenotype_phase_plane(model, "EX_glc__D_e", "EX_o2_e", n_processes=1,
                                reaction1_npoints=100, reaction2_npoints=100)
print("took %.2f seconds with 1 process" % (time() - start_time))
start_time = time()
calculate_phenotype_phase_plane(model, "EX_glc__D_e", "EX_o2_e", n_processes=4,
                                reaction1_npoints=100, reaction2_npoints=100)
print("took %.2f seconds with 4 process" % (time() - start_time))









    



took 0.40 seconds with 1 process
took 0.21 seconds with 4 process