- Author:
- WeiweiAi <wai484@aucklanduni.ac.nz>
- Date:
- 2021-07-19 18:24:55+12:00
- Desc:
- Output rho_vCa, and add input inhPump to inhibit J_Ca,pump for Fig2;
Make K_Cahalf control para for Fig 7;
Add Unit_uSMC.cellml to decouple Cai.
Add Multi_stim, Vramp and Nai experiments;
Add original figures and derived data;
Add simulation and plot scripts
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/6bb/rawfile/77e3c05d5c087de8b306f4578136aebd2c365954/Simulation/src/Fig4_plot.py
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
# The prefix of the saved output file name
prefilenames = ['simFig4A','simFig4B']
ofilenames = ['fig4A', 'fig4B']
# Figure name
prefig = 'Fig4'
figfile = 'sim%s' % prefig
# Set figure dimension (width, height) in inches.
fw, fh = 6, 6
fig = plt.figure(figsize=(fw,fh))
ax, lns = {}, {}
# 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']
# Set subplots
lfontsize, labelfontsize = 12, 12 # legend, label fontsize
t_ss = 0.2
# Read data from the files
x_name = 'time'
y_name = 'Cai'
y_labels = ['[Ca]$_i$ (nM)']
Nai=[ 2.9836,16.55]
# Set subplots
subpRow, subpCol = len(prefilenames), 1
for h, plotN in enumerate(prefilenames):
ax[h] = fig.add_subplot(subpRow, subpCol, h+1)
ofilename ='../originalData/%s.csv' % ofilenames[h]
odata = pd.read_csv(ofilename)
ox_data = odata['x']
oy_data = odata['Curve1']
ax[h].plot(ox_data, oy_data, '.', color=cycle[0], label = 'Bursztyn_et_al_uSMC @ Nai=16.55mM')
for i, iNai in enumerate(Nai):
filename='../simulatedData/%s_%d.csv' % (prefilenames[h],i)
data = pd.read_csv(filename)
x_data = data[x_name]- t_ss
y_data = data[y_name]*1000000
ax[h].plot(x_data, y_data, color=cycle[i], label = '@ Nai=%.2fmM' % (iNai))
plt.tick_params(direction='in', axis='both')
ax[h].legend(loc = 'best', fontsize=lfontsize, frameon=False)
ax[h].set_xlabel ('Time (s)', fontsize= labelfontsize)
ax[h].set_ylabel (y_labels[0], fontsize= labelfontsize)
if h == 0:
ax[h].set_title('%s in the primary publication' % (prefig))
figfiles = '../%s.png' % (figfile)
plt.savefig(figfiles)
plt.show()
