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R4670/plot/plot_Ih_kinetics.py
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plot_Ih_kinetics.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
# @Author: Theo Lemaire
# @Date: 2016-10-11 20:35:38
# @Email: theo.lemaire@epfl.ch
# @Last Modified by: Theo Lemaire
# @Last Modified time: 2018-09-21 16:11:08
""" Plot the voltage-dependent kinetics of the hyperpolarization-activated
cationic current found in thalamo-cortical neurons. """
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.cm as cm
from matplotlib.colors import LogNorm
from PySONIC.neurons import ThalamoCortical
from PySONIC.utils import rescale
# -------------- SIMULATION -----------------
# Create channels mechanism
neuron = ThalamoCortical()
# Input vectors
nV = 100
nC = 10
CCa_min = 0.01 # uM
CCa_max = 10 # um
Vm = np.linspace(-100, 50, nV) # mV
CCa = np.logspace(np.log10(CCa_min), np.log10(CCa_max), nC) # uM
# Output matrix: relative activation (0-2)
BA = neuron.betao(Vm) / neuron.alphao(Vm)
P0 = neuron.k2 / (neuron.k2 + neuron.k1 * (CCa * 1e-6)**4)
gH_rel = np.empty((nV, nC))
for i in range(nC):
O_form = neuron.k4 / (neuron.k3 * (1 - P0[i]) + neuron.k4 * (1 + BA))
OL_form = (1 - O_form * (1 + BA))
gH_rel[:, i] = O_form + 2 * OL_form
mymap = cm.get_cmap('viridis')
sm = plt.cm.ScalarMappable(cmap=mymap, norm=LogNorm(CCa_min, CCa_max))
sm._A = []
fs = 18
fig, ax = plt.subplots(figsize=(8, 5))
ax.set_title('global activation', fontsize=fs)
ax.set_xlabel('$V_m\ (mV)$', fontsize=fs)
ax.set_ylabel('$(O + 2O_L)_{\infty}$', fontsize=fs)
ax.set_yticks([0, 1, 2])
for i in range(nC):
ax.plot(Vm, gH_rel[:, i], linewidth=2,
c=mymap(rescale(np.log10(CCa[i]), np.log10(CCa_min), np.log10(CCa_max))))
fig.subplots_adjust(right=0.85)
cbar_ax = fig.add_axes([0.87, 0.1, 0.02, 0.8])
fig.add_axes()
fig.colorbar(sm, cax=cbar_ax)
cbar_ax.set_ylabel('$[Ca^{2+}_i]\ (uM)$', fontsize=fs)
plt.show()
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