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:
| 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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 | 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:
