Python scan_range Examples

Example #1

File: Scan0A.py Project: CounterZone/BioDS

import tools
from DS_solver import bioDS
import numpy as np
import matplotlib.pyplot as plt
test=bioDS(path='SinIR/')
test.load()

cc=tools.scan_range(test,parameter='Spo0A_p',exp='Ptap',space=np.linspace(0,4,10),save=False,savelog=False,show=False,time=60,fname='normal_pos_2.pdf')
test.set('trr',0.15)

dd=tools.scan_range(test,parameter='Spo0A_p',exp='Ptap',space=np.linspace(0,4,10),save=False,savelog=False,show=False,time=60,fname='trans_pos_2.pdf')


test=bioDS(path='SinIR2/')
test.load()

ee=tools.scan_range(test,parameter='Spo0A_p',exp='Ptap',space=np.linspace(0,4,10),save=False,savelog=False,show=False,time=60,fname='trans_pos_2.pdf')



plt.plot(np.linspace(0,4,10),cc[0],"b--",linewidth=0.5)
plt.plot(np.linspace(0,4,10),cc[1],"b--",linewidth=0.5)
plt.plot(np.linspace(0,4,10),cc[2],label="Normal_Pos",linewidth=1.0)
plt.fill_between(np.linspace(0,4,10),cc[0],cc[1],alpha=0.1)

plt.plot(np.linspace(0,4,10),dd[0],"b--",linewidth=0.5)
plt.plot(np.linspace(0,4,10),dd[1],"b--",linewidth=0.5)
plt.plot(np.linspace(0,4,10),dd[2],label="trans_Pos",linewidth=1.0)
plt.fill_between(np.linspace(0,4,10),dd[0],dd[1],alpha=0.1)

Example #2

File: script_2.py Project: CounterZone/BioDS

####



import tools
from DS_solver import bioDS
import numpy as np
import matplotlib.pyplot as plt

kinc=bioDS(path="KinC_2/")
kinc.load()
k2=[300,200,100,50,20]
cs={}
kincc=bioDS(path="KinC_0/")
kincc.load()
cc=tools.scan_range(kincc,parameter='viKinA',exp='Spo0A_p',space=np.linspace(0,20,60),save=False,savelog=False,show=False,time=30)
for i in k2:
	print(i)
	kinc.set("k2",i)
	cs[i]=tools.scan_range(kinc,parameter='viKinA',exp='Spo0A_p',space=np.linspace(0,20,60),save=True,show=False,fname="range_k2_%d"%i,savelog=False,time=30)
for i in k2:
	plt.plot(np.linspace(0,20,60),cs[i][0],"b--",linewidth=0.5)
	plt.plot(np.linspace(0,20,60),cs[i][1],"b--",linewidth=0.5)
	plt.plot(np.linspace(0,20,60),cs[i][2],label="k2=%d"%i,linewidth=1.0)
	plt.fill_between(np.linspace(0,20,60),cs[i][0],cs[i][1],alpha=0.1)

plt.plot(np.linspace(0,20,60),cc[0],"b--",linewidth=0.5)
plt.plot(np.linspace(0,20,60),cc[1],"b--",linewidth=0.5)
plt.plot(np.linspace(0,20,60),cc[2],label="KinA",linewidth=1.0)
plt.fill_between(np.linspace(0,20,60),cc[0],cc[1],alpha=0.1)

Example #3

File: script_s.py Project: CounterZone/BioDS

import tools
from DS_solver import bioDS
import numpy as np
import matplotlib.pyplot as plt
sc=bioDS(path="KinC_3_ir/")
sc.load()
sa=bioDS(path="KinA_0/")
sa.load()
sa.add(parameters="../s_parameter",reactions="../s_reaction")
sc.add(parameters="../s_parameter",reactions="../s_reaction")


atap=tools.scan_range(sa,parameter='viKinA',exp='ptapa',space=np.linspace(0,20,60),save=False,savelog=False,show=False,time=30)
aspo=tools.scan_range(sa,parameter='viKinA',exp='pspoIIg',space=np.linspace(0,20,60),save=False,savelog=False,show=False,time=30)
ctap=tools.scan_range(sc,parameter='viKinA',exp='ptapa',space=np.linspace(0,20,60),save=False,savelog=False,show=False,time=30)
cspo=tools.scan_range(sc,parameter='viKinA',exp='pspoIIg',space=np.linspace(0,20,60),save=False,savelog=False,show=False,time=30)

plt.plot(np.linspace(0,20,60),atap[0],"b--",linewidth=0.5)
plt.plot(np.linspace(0,20,60),atap[1],"b--",linewidth=0.5)
plt.plot(np.linspace(0,20,60),atap[2],label="KinA_tap",linewidth=2.0)
plt.fill_between(np.linspace(0,20,60),atap[0],atap[1],alpha=0.1)

plt.plot(np.linspace(0,20,60),aspo[0],"b--",linewidth=0.5)
plt.plot(np.linspace(0,20,60),aspo[1],"b--",linewidth=0.5)
plt.plot(np.linspace(0,20,60),aspo[2],label="KinA_spo",linewidth=2.0)
plt.fill_between(np.linspace(0,20,60),aspo[0],aspo[1],alpha=0.1)

plt.plot(np.linspace(0,20,60),ctap[0],"b--",linewidth=0.5)

Example #4

File: script_s2.py Project: CounterZone/BioDS

####



import tools
from DS_solver import bioDS
import numpy as np
import matplotlib.pyplot as plt
kinc=bioDS(path="KinC_4_ir/")
kinc.load()
kina=bioDS(path="KinC_3_ir/")
kina.load()


cc=tools.scan_range(kinc,parameter='viKinA',exp='Spo0A_p',space=np.linspace(0,20,60),save=False,savelog=False,show=False,time=30)
aa=tools.scan_range(kina,parameter='viKinA',exp='Spo0A_p',space=np.linspace(0,20,60),save=False,savelog=False,show=False,time=30)

plt.plot(np.linspace(0,20,60),cc[0],"b--",linewidth=0.5)
plt.plot(np.linspace(0,20,60),cc[1],"b--",linewidth=0.5)
plt.plot(np.linspace(0,20,60),cc[2],label="0B-",linewidth=2.0)
plt.fill_between(np.linspace(0,20,60),cc[0],cc[1],alpha=0.1)
plt.plot(np.linspace(0,20,60),aa[0],"b--",linewidth=0.5)
plt.plot(np.linspace(0,20,60),aa[1],"b--",linewidth=0.5)
plt.plot(np.linspace(0,20,60),aa[2],label="KinC",linewidth=2.0)
plt.fill_between(np.linspace(0,20,60),aa[0],aa[1],alpha=0.1)
plt.legend(bbox_to_anchor=(0.15, 1))
plt.plot([0,20],[0.4,0.4],"b--")
plt.plot([0,20],[0.8,0.8],"b--")
plt.plot([0,20],[1.5,1.5],"b--")
plt.xlabel("ViKin")

Example #5

File: hill.py Project: CounterZone/BioDS

from DS_solver import bioDS
import numpy as np
import matplotlib.pyplot as plt
import tools
hill=bioDS(path="hill/")
hill.parameters["Spo0A_p"]=0
hill.parameters["kdeg"]=0.7
hill.add(parameters="../s_parameter",reactions="../s_reaction")
atap=tools.scan_range(hill,parameter='Spo0A_p',exp='ptapa',space=np.linspace(0,5,60),save=False,savelog=False,show=False,time=15,period=0.2)
aspo=tools.scan_range(hill,parameter='Spo0A_p',exp='pspoIIg',space=np.linspace(0,5,60),save=False,savelog=False,show=False,time=15,period=0.2)
plt.plot(np.linspace(0,5,60),atap[2],label="tapA")
plt.plot(np.linspace(0,5,60),aspo[2],label="spoIIg")
v_line=[0.4,0.8,2.3]
ye=list(plt.axis())[-2:]
for i in v_line:
	te=np.ones(2)*i
	plt.plot(te,ye,'k--')
plt.xlabel("Spo0A_p")
plt.ylabel("Reporter")
plt.legend(bbox_to_anchor=(0.95, 0.95))
plt.savefig("hill/hill.pdf")
plt.show()