- Author:
- WeiweiAi <wai484@aucklanduni.ac.nz>
- Date:
- 2022-07-28 12:05:55+12:00
- Desc:
- Fixed the link
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/8af/rawfile/1b1a07491a4d102536a3f7e25957ca2810d6ed76/Simulation/src/plotFig4.py
# importing modules
import sys as sys
import os
import pandas as pd
import matplotlib.pyplot as plt
# Getting the name of the directory where this file is present.
current = os.path.dirname(os.path.realpath(__file__)) # src
# Getting the parent directory name where the current directory is present.
parent = os.path.dirname(current) # Simulation
# Getting the grandparent directory name
gparent = os.path.dirname(parent) # RecruitmentSynchronization_SMCs
# The path where the plotExp.py is saved
mpath = gparent + '\\cellLib\\Scripts'
# appending a path
sys.path.append(mpath)
import plotExp
# The properties of traces
colors=plt.rcParams['axes.prop_cycle'].by_key()['color']
lines = ['-','--','-.',':']
markers = ['.',',','o','+','x','d']
# Figure file name and titles
figfiles=parent+'\\simFig4.png'
fig_title = 'Primary Fig 4'
plot_title =['Voltage dependency','Transfer function']
labels = ['Original $Q$','CellML $Q$','Original $P$','CellML $P$','CellML $Q_{ss}$','CellML $P_{ss}$']
# Data source
dfolder_original=parent+'\\originalData\\'
ofilenames=['Fig4A_Q.csv','Fig4B.csv','Fig4A_P.csv']
dfilename_sim=parent+'\\simulatedData\\simFig4.csv'
x_var_org ='x'
y_var_org ='Curve1'
x_var_sim = ['clamp_para/V_actTest','output_10/Q','clamp_para/V_actTest']
y_vars_sim = ['output_10/Q','output_10/P_o','output_10/P_o']
ss_vars_sim = ['output_10/Q_ss','output_10/P_ss','output_10/P_ss']
x_label=['Voltage (mV)','Charge ($nC/\mu F$)','Voltage (mV)']
y_label=['Charge ($nC/\mu F$)','Ca Release (normalized)','Ca Release (normalized)']
Qmax=23.1
# Build the traces
number_trace = 3
number_plot = len(y_vars_sim)
trace = [[0] * number_trace for i in range(number_plot)]
data = pd.read_csv(dfilename_sim)
for plotid, y_var_sim in enumerate(y_vars_sim):
odata = pd.read_csv(dfolder_original+ofilenames[plotid])
ox_data=odata[x_var_org].values
oy_data=odata[y_var_org].values
if y_var_sim=='output_10/Q':
y_data=data[y_var_sim].values*Qmax
ss_data=data[ss_vars_sim[plotid]].values*Qmax
else:
y_data=data[y_var_sim].values/0.629121513819098
ss_data=data[ss_vars_sim[plotid]].values/0.629121513819098
if x_var_sim[plotid]=='output_10/Q':
x_data=data[x_var_sim[plotid]].values*Qmax
else:
x_data=data[x_var_sim[plotid]].values
if plotid<2:
trace[plotid][0]={'dataX': ox_data, 'dataY': oy_data, 'lname': labels[plotid*2], 'linestyle':lines[1], 'marker':markers[0], 'linecolor':colors[plotid],'y2':False}
trace[plotid][1]={'dataX': x_data, 'dataY': y_data, 'lname': labels[plotid*2+1], 'linestyle':lines[0], 'marker':None, 'linecolor':colors[plotid],'y2':False}
trace[plotid][2]={'dataX': x_data, 'dataY': ss_data, 'lname': labels[plotid+4], 'linestyle':lines[1], 'marker':markers[4], 'linecolor':colors[plotid],'y2':False}
else:
otrace={'dataX': ox_data, 'dataY': oy_data, 'lname': labels[2], 'linestyle':lines[1], 'marker':markers[0], 'linecolor':colors[1],'y2':True}
ntrace={'dataX': x_data, 'dataY': y_data, 'lname': labels[3], 'linestyle':lines[0], 'marker':None, 'linecolor':colors[1],'y2':True}
strace={'dataX': x_data, 'dataY': ss_data, 'lname': labels[5], 'linestyle':lines[1], 'marker':markers[4],'linecolor':colors[1],'y2':True}
# Build the plots
# maxH=8.75 inches, width 2.63-7.5
rows,cols = 1,2
left = 0.125 # the left side of the subplots of the figure,0.125
right = 0.9 # the right side of the subplots of the figure,0.9
bottom = 0.15 # the bottom of the subplots of the figure, 0.1
top = 0.7 # the top of the subplots of the figure 0.9
wspace = 0.5 # the amount of width reserved for space between subplots,
# expressed as a fraction of the average axis width, 0.2
hspace = 0.1 # the amount of height reserved for space between subplots,
# expressed as a fraction of the average axis height, 0.2
lgdfont, labelfont =10, 10
width, height= cols*3.5, rows*4
figs ={ 'width':width, 'height': height, 'rows': rows, 'cols': cols,'left':left,'bottom':bottom,'right':right,'top':top,'wspace': wspace,'hspace': hspace,'fig_title':fig_title,'title_y':1.0}
plots=[]
for id in range(2):
colid = id%2
rowid = id//2
if id == 0:
lgdshow = True
bbox_to_anchor = (1.2,1.25)
trace[id].append(otrace)
trace[id].append(ntrace)
trace[id].append(strace)
else:
lgdshow = False
bbox_to_anchor = None
if id==0:
iplot={'rowid':rowid, 'colid':colid, 'xlabel': x_label[id], 'ylabel':y_label[id], 'twiny':True, 'ylabel2':y_label[id+1],'labelcolor':colors[1],
'lgdshow': lgdshow, 'lgdloc':'center', 'bbox_to_anchor':bbox_to_anchor,'lgdncol': 2, 'lgdfont':lgdfont, 'labelfont': labelfont,
'setxlim': False, 'xmin':0, 'xmax': 1, 'setylim': False,'ymin':0, 'ymax':1, 'grid': True, 'gridaxis': 'both', 'plot_title': plot_title[id],
'traces':trace[id]
}
else:
iplot={'rowid':rowid, 'colid':colid, 'xlabel': x_label[id], 'ylabel':y_label[id+1], 'twiny':False, 'ylabel2':y_label[id],'labelcolor':colors[1],
'lgdshow': lgdshow, 'lgdloc':'center', 'bbox_to_anchor':bbox_to_anchor,'lgdncol': 2, 'lgdfont':lgdfont, 'labelfont': labelfont,
'setxlim': False, 'xmin':0, 'xmax': 1, 'setylim': False,'ymin':0, 'ymax':1, 'grid': True, 'gridaxis': 'both', 'plot_title': plot_title[id],
'traces':trace[id]
}
plots.append(iplot)
ids = range(len(y_vars_sim))
subfigs={ids: plots for ids, plots in zip(ids, plots)}
fig,axs=plotExp.plotExp(figs,subfigs,figfiles)
