- Author:
- WeiweiAi <wai484@aucklanduni.ac.nz>
- Date:
- 2022-03-31 10:48:40+13:00
- Desc:
- Add open channel IV of HH models; Add simulation and plot python scripts
- Permanent Source URI:
- https://models.fieldml.org/workspace/64f/rawfile/ab2962b8796666ad9938a2577611c954f006b5fd/sed-ml/anodeGating_plot.py
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
# The prefix of the saved output file name
prefilename = 'simFig22'
V_initial = [30]
# Figure name
prefig = 'anodeGating'
figfile = '%s.png' % prefig
# Set figure dimension (width, height) in inches.
fw, fh = 6, 9
fig = plt.figure(figsize=(fw,fh))
# Set subplots
subpRow, subpCol = 3, 1
lns = {}
lfontsize, labelfontsize = 10, 10 # legend, label fontsize
# This gives list with the colors from the cycle, which you can use to iterate over.
cycle = plt.rcParams['axes.prop_cycle'].by_key()['color']
# Read data from the files
plotindex = [1, 2, 3]
x_name = 'outputs/time'
y_names =[['outputs/minus_V','outputs/m','outputs/h','outputs/n',],['outputs/minus_V','outputs/gNa','outputs/gK',],
['outputs/minus_V','outputs/INa','outputs/IK','outputs/Ileak','outputs/Ii']]
yl_names =[['-V','m','h','n',],['-V','$g_{Na}$','$g_{K}$',],
['-V','$I_{Na}$','$I_{K}$','$I_{l}$','$I_{i}$']]
y_labels =[['-V (mV)','gating'], ['-V (mV)','conductance'], ['-V (mV)','Currents']]
rol=int(25*100)
w, h = 2, len(y_labels)
ax = [[0 for x in range(w)] for y in range(h)]
for j, iV_initial in enumerate(V_initial):
filename ='%s_(%d)mV.csv' % (prefilename, iV_initial)
data = pd.read_csv(filename)
x_data = data[x_name][0:rol]
for i, y_name in enumerate(y_names):
for m, iy_name in enumerate(y_name):
y_data = data[iy_name][0:rol]
if m == 0:
ax[i][0] = fig.add_subplot(subpRow, subpCol, plotindex[i])
ax[i][0].plot(x_data, y_data,'-.', color=cycle[m],label='%s' % (yl_names[i][m]))
ax[i][0].set_ylabel (y_labels[i][0], fontsize= labelfontsize)
ax[i][0].tick_params(direction='in', axis='both')
ax[i][0].grid(axis='x',linestyle='-.')
elif m == 1:
ax[i][1] = ax[i][0].twinx()
lns[m]= ax[i][1].plot(x_data, y_data, color=cycle[m], label='%s' % (yl_names[i][m]))
sumlns=lns[m]
ax[i][1].set_ylabel (y_labels[i][1], fontsize= labelfontsize)
ax[i][1].tick_params(direction='in', axis='both')
else:
lns[m]= ax[i][1].plot(x_data, y_data, color=cycle[m], label='%s' % (yl_names[i][m]))
sumlns=sumlns+lns[m]
if plotindex[i] in [3]:
ax[i][0].set_xlabel ('time(ms)', fontsize= labelfontsize)
else:
ax[i][0].set_xticklabels([])
ax[i][1].legend(sumlns, yl_names[i][1:], frameon=False, loc= 'upper right')
plt.savefig(figfile)
plt.show()
