- Author:
- nima <nafs080@aucklanduni.ac.nz>
- Date:
- 2021-09-14 11:51:06+12:00
- Desc:
- matplotlib.use('agg') is added
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/648/rawfile/2408209b761288e46e32e5ad86d7ee30ae110579/Figure1.py
# To reproduce Figure 1 in the associated Physiome paper,
# execute this script from the command line:
#
# cd [PathToThisFile]
# [PathToOpenCOR]/pythonshell Figure1.py
import matplotlib
matplotlib.use('agg')
import numpy as np
import matplotlib.pyplot as plt
import opencor as opencor
# load the reference model
simulation = opencor.open_simulation("HumanSAN_Fabbri_Fantini_Wilders_Severi_2017.sedml")
data = simulation.data()
data.set_ending_point(1.6)
data.set_point_interval(0.001)
results = dict()
simulation.reset(True)
for i in range(29):
simulation.run()
simulation.clear_results()
simulation.run()
ds = simulation.results().data_store()
results[0] = ds.voi_and_variables()["environment/time"].values()
results[1] = ds.voi_and_variables()["Membrane/V_ode"].values()
results[2] = ds.voi_and_variables()["Ca_dynamics/Cai"].values()
# define the x and y axis and match the units
X = results[0] * 1000
Y1 = results[1]
Y2 = results[2] * 1e6
plt.figure(figsize=(11, 8))
plt.subplot(2, 1, 1)
plt.plot(X, Y1, 'navy', linestyle='-', label='', linewidth=3)
plt.xlim(0, 1600, 1000)
plt.yticks(np.arange(-70, 40, 20))
plt.ylabel('V$_m$ (mV)', fontsize=22)
plt.tick_params(axis='x', labelsize=18)
plt.tick_params(axis='y', labelsize=18)
plt.title('A', loc='left', y=1.05, x=-0.06, fontsize=22)
plt.tight_layout()
plt.subplot(2, 1, 2)
plt.plot(X, Y2, 'navy', linestyle='-', label='', linewidth=3)
plt.xlim(0, 1600, 1000)
plt.yticks(np.arange(50, 300, 50))
plt.ylabel('[Ca$^{2+}$]$_i$ (nM)', fontsize=22)
plt.xlabel('Time (ms)', fontsize=22)
plt.title('B', loc='left', y=1.05, x=-0.06, fontsize=22)
plt.tick_params(axis='x', labelsize=18)
plt.tick_params(axis='y', labelsize=18)
plt.subplots_adjust(bottom=0.5, right=0.8, top=1)
plt.tight_layout(pad=0.4, w_pad=0.5, h_pad=1.0)
plt.savefig('Figure1.png')
