Plotting Bar graph of Species Concentrations in Tellurium

Originally Posted on October 20, 2017 by hsauro

I had a model with 27 floating species and I wanted to plot the steady-state concentrations on a histogram where the labels were the names of the different species. Here is a general purpose script that will do that:

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def plotFloatingSpecies (r, width=12, height=6):     import matplotlib.pyplot as plt     xlabels = r.getFloatingSpeciesIds()     concs = r.getFloatingSpeciesConcentrations()     plt.figure(figsize=(width,height))     plt.bar(xlabels, concs, label=xlabels)     plt.xticks(range (len (xlabels)), xlabels, ha='right', rotation=45)

The function has a default width and height for the resulting plot. The default widens the usual size so that the labels don’t collide. The first argument is the libroadrunner instance.  To given a contrived example, the following is a model of 8 floating species that form a linear chain governed by simple irreversible mass-action kinetics.

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import tellurium as te import roadrunner   def plotFloatingSpecies (r, width=12, height=6):     import matplotlib.pyplot as plt     xlabels = r.getFloatingSpeciesIds()     concs = r.getFloatingSpeciesConcentrations()     plt.figure(figsize=(width,height))         plt.bar(xlabels, concs, label=xlabels)     plt.xticks(range (len (xlabels)), xlabels,  ha='right', rotation=45)       r = te.loada("""      $Xo -> S1; k1*Xo;       S1 -> S2;  k2*S1;       S2 -> S3;  k3*S2;       S3 -> S4;  k3*S3;       S4 -> S5;  k4*S4;       S5 -> S6;  k5*S5;       S6 -> S7;  k4*S6;       S7 -> S8;  k3*S7;       S8 -> ;    k4*S8;              k1 = 0.3; k2 = 0.5; k3 = 0.27; k4 = 0.9; k5 = 0.14       Xo = 10; """)   r.steadyState() plotFloatingSpecies (r, width=6, height=3)

The resulting plot is shown below: