Location: Computational analysis of the human sinus node action potential @ 7cb8a9d44ad7 / Figure7-new.py

Author:
nima <nafs080@aucklanduni.ac.nz>
Date:
2021-06-19 09:23:55+12:00
Desc:
1 script instead of 2
Permanent Source URI:
https://staging.physiomeproject.org/workspace/648/rawfile/7cb8a9d44ad7e22d7ee5ee37d836a6f97e05758f/Figure7-new.py
Compare... Download Source 

# To reproduce Figure 3 in the associated Physiome paper,
# execute this script from the command line:
#
#   cd [PathToThisFile]
#   [PathToOpenCOR]/pythonshell Figure7.py

import matplotlib

matplotlib.use('agg')

import numpy as np
import matplotlib.pyplot as plt
from matplotlib.patches import Rectangle

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(2.5)
data.set_point_interval(0.001)

simulation.reset(True)

results = np.zeros((25, 2501))

for i in range(0,1):
    simulation.run()
    ds = simulation.results().data_store()
    results[0] = ds.voi_and_variables()["environment/time"].values()

for i in range(0,25):
    simulation.run()
    simulation.clear_results()

simulation.run()
ds = simulation.results().data_store()
results[1] = ds.voi_and_variables()["Membrane/V"].values()
results[4] = ds.voi_and_variables()["i_NaK/i_NaK"].values()
results[7] = ds.voi_and_variables()["Membrane/i_tot"].values()
results[10] = ds.voi_and_variables()["i_Ks/i_Ks"].values()
results[13] = ds.voi_and_variables()["i_f/i_f"].values()
results[16] = ds.voi_and_variables()["i_KACh/i_KACh"].values()
results[19] = ds.voi_and_variables()["i_CaL/i_CaL"].values()
results[22] = ds.voi_and_variables()["Ca_intracellular_fluxes/j_up"].values()

simulation.reset(True)


for i in range(0,14):
    data.constants()["Rate_modulation_experiments/ACh"] = 1e-5
    simulation.run()
    simulation.clear_results()

simulation.run()
ds = simulation.results().data_store()
results[2] = ds.voi_and_variables()["Membrane/V"].values()
results[5] = ds.voi_and_variables()["i_NaK/i_NaK"].values()
results[8] = ds.voi_and_variables()["Membrane/i_tot"].values()
results[11] = ds.voi_and_variables()["i_Ks/i_Ks"].values()
results[14] = ds.voi_and_variables()["i_f/i_f"].values()
results[17] = ds.voi_and_variables()["i_KACh/i_KACh"].values()
results[20] = ds.voi_and_variables()["i_CaL/i_CaL"].values()
results[23] = ds.voi_and_variables()["Ca_intracellular_fluxes/j_up"].values()



simulation.reset(True)
for i in range(0,13):
    data.constants()["Rate_modulation_experiments/Iso_1_uM"] = 1
    simulation.run()
    simulation.clear_results()

simulation.run()
ds = simulation.results().data_store()
results[3] = ds.voi_and_variables()["Membrane/V"].values()
results[6] = ds.voi_and_variables()["i_NaK/i_NaK"].values()
results[9] = ds.voi_and_variables()["Membrane/i_tot"].values()
results[12] = ds.voi_and_variables()["i_Ks/i_Ks"].values()
results[15] = ds.voi_and_variables()["i_f/i_f"].values()
results[18] = ds.voi_and_variables()["i_KACh/i_KACh"].values()
results[21] = ds.voi_and_variables()["i_CaL/i_CaL"].values()
results[24] = ds.voi_and_variables()["Ca_intracellular_fluxes/j_up"].values()


# define the x and y axis and match the units
X = results[0]*1000
Y1 = results[1]
Y2 = results[2]
Y3 = results[3]
Y4 = results[4]*1000/57
Y5 = results[5]*1000/57
Y6 = results[6]*1000/57
Y7 = results[7]*1000/57
Y8 = results[8]*1000/57
Y9 = results[9]*1000/57
Y10 = results[10]*1000/57
Y11 = results[11]*1000/57
Y12 = results[12]*1000/57
Y13 = results[13]*1000/57
Y14 = results[14]*1000/57
Y15 = results[15]*1000/57
Y16 = results[16]*1000/57
Y17 = results[17]*1000/57
Y18 = results[18]*1000/57
Y19 = results[19]*1000/57
Y20 = results[20]*1000/57
Y21 = results[21]*1000/57
Y22 = results[22]
Y23 = results[23]
Y24 = results[24]



plt.figure(figsize=(17,17))
plt.subplot(4,2,1)

plt.plot(X, Y1, 'navy',linestyle='-',  label = 'CTRL', linewidth= 3)
plt.plot(X, Y2, 'red',linestyle='-',  label = '10 nM ACh', linewidth= 3)
plt.plot(X, Y3, 'green',linestyle='-',  label = '1 \u03BCM Iso', linewidth= 3)


plt.grid()
plt.xlim(0, 2470)
plt.xticks(np.arange(0,2470,500))
plt.ylim(-100,50)
plt.yticks(np.arange(-100,60,50))

plt.tick_params(axis='both', labelsize=14)
plt.ylabel ('V$_m$ (mV)', fontsize=16)
plt.title('A', loc= 'left', y = 1.05, x= -0.06, fontsize='20')
plt.legend(bbox_to_anchor=(0., 0.92, 1, 0.1), loc='best',fontsize=14, ncol=10, mode="expand")

plt.subplot(4,2,2)
plt.plot(X, Y4, 'navy',linestyle='-',  label = 'CTRL', linewidth= 3)
plt.plot(X, Y5, 'red',linestyle='-',  label = '10 nM ACh', linewidth= 3)
plt.plot(X, Y6, 'green',linestyle='-',  label = '1 ${mu}$M Iso', linewidth= 3)




plt.grid()
plt.xlim(0, 2470)
plt.xticks(np.arange(0,2470,500))
plt.ylim(0,0.3)
plt.yticks(np.arange(0, 0.4,0.1))

plt.tick_params(axis='both', labelsize=14)
plt.ylabel ('I$_{NaK}$ (pA/pF)', fontsize=16)
plt.title('E', loc= 'left', y = 1.05, x= -0.06, fontsize='20')


plt.subplot(4,2,3)
plt.plot(X, Y7, 'navy',linestyle='-',  label = 'CTRL', linewidth= 3)
plt.plot(X, Y8, 'red',linestyle='-',  label = '10 nM ACh', linewidth= 3)
plt.plot(X, Y9, 'green',linestyle='-',  label = '1 \u03BC M Iso', linewidth= 3)




plt.grid()
plt.xlim(0, 2470)
plt.xticks(np.arange(0,2470,500))
plt.ylim(-15,5)
plt.yticks(np.arange(-15,10,5))

plt.tick_params(axis='both', labelsize=14)
plt.ylabel ('I$_{tot}$ (pA/pF)', fontsize=16)
plt.title('B', loc= 'left', y = 1.05, x= -0.06, fontsize='20')


plt.subplot(4,2,4)
plt.plot(X, Y10, 'navy',linestyle='-',  label = 'CTRL', linewidth= 3)
plt.plot(X, Y11, 'red',linestyle='-',  label = '10 nM ACh', linewidth= 3)
plt.plot(X, Y12, 'green',linestyle='-',  label = '1 ${mu}$M Iso', linewidth= 3)




plt.grid()
plt.xlim(0, 2470)
plt.xticks(np.arange(0,2470,500))
plt.ylim(-0.2,0.4)
plt.yticks(np.arange(-0.2,0.5,0.2))

plt.tick_params(axis='both', labelsize=14)
plt.ylabel ('I$_{Ks}$ (pA/pF)', fontsize=16)
plt.title('F', loc= 'left', y = 1.05, x= -0.06, fontsize='20')

plt.subplot(4,2,5)
plt.plot(X, Y13, 'navy',linestyle='-',  label = 'CTRL', linewidth= 3)
plt.plot(X, Y14, 'red',linestyle='-',  label = '10 nM ACh', linewidth= 3)
plt.plot(X, Y15, 'green',linestyle='-',  label = '1 ${mu}$M Iso', linewidth= 3)

plt.grid()
plt.xlim(0, 2470)
plt.xticks(np.arange(0,2470,500))
plt.ylim(-0.05,0.05)
plt.yticks(np.arange(-0.05,0.06,0.05))

plt.tick_params(axis='both', labelsize=14)
plt.ylabel ('I$_{f}$ (pA/pF)', fontsize=16)
plt.title('C', loc= 'left', y = 1.05, x= -0.06, fontsize='20')

plt.subplot(4,2,6)
plt.plot(X, Y16, 'navy',linestyle='-',  label = 'CTRL', linewidth= 3)
plt.plot(X, Y17, 'red',linestyle='-',  label = '10 nM ACh', linewidth= 3)
plt.plot(X, Y18, 'green',linestyle='-',  label = '1 ${mu}$M Iso', linewidth= 3)




plt.grid()
plt.xlim(0, 2470)
plt.xticks(np.arange(0,2470,500))
plt.ylim(0,0.2)
plt.yticks(np.arange(0,0.25,0.05))

plt.tick_params(axis='both', labelsize=14)
plt.ylabel ('I$_{K,ACh}$ (pA/pF)', fontsize=16)
plt.title('G', loc= 'left', y = 1.05, x= -0.06, fontsize='20')

plt.subplot(4,2,7)
plt.plot(X, Y19, 'navy',linestyle='-',  label = 'CTRL', linewidth= 3)
plt.plot(X, Y20, 'red',linestyle='-',  label = '10 nM ACh', linewidth= 3)
plt.plot(X, Y21, 'green',linestyle='-',  label = '1 ${mu}$M Iso', linewidth= 3)




plt.grid()
plt.xlim(0, 2470)
plt.xticks(np.arange(0,2470,500))
plt.ylim(-15,1)
plt.yticks(np.arange(-15,2,5))
plt.xlabel ('Time (ms)',fontsize=16)
plt.tick_params(axis='both', labelsize=14)
plt.ylabel ('I$_{CaL}$ (pA/pF)', fontsize=16)
plt.title('D', loc= 'left', y = 1.05, x= -0.06, fontsize='20')

plt.subplot(4,2,8)
plt.plot(X, Y22, 'navy',linestyle='-',  label = 'CTRL', linewidth= 3)
plt.plot(X, Y23, 'red',linestyle='-',  label = '10 nM ACh', linewidth= 3)
plt.plot(X, Y24, 'green',linestyle='-',  label = '1 ${mu}$M Iso', linewidth= 3)




plt.grid()
plt.xlim(0, 2470)
plt.xticks(np.arange(0,2470,500))
plt.ylim(0,1.5)
plt.yticks(np.arange(0,1.6,0.5))
plt.xlabel ('Time (ms)',fontsize=16)
plt.tick_params(axis='both', labelsize=14)
plt.ylabel ('J$_{up}$ (mM/s)', fontsize=16)
plt.title('H', loc= 'left', y = 1.05, x= -0.06, fontsize='20')


plt.tight_layout(pad=0.5, w_pad=3, h_pad=3)
plt.savefig('figure7-new.png')