def discreet(py, pt, *string, **kwargs):
mode = kwargs.get('mode', 'limit')
(m6, m7, m12, m1, n1) = prc.evmode(mode, py)
t = [pt, pt, pt, pt]
px = [
prc.discr(py[1], m1, n1),
prc.discr(py[6], m6),
prc.discr(py[7], m7),
prc.discr(py[12], m12)
]
colour = [c.blood, 'navy', c.darkorange, c.green]
label = ['IKKa', 'NF$\kappa$B', 'A20', 'NF$\kappa$B:I$\kappa$B']
lstyle = ['-', '--', '-.', ':']
xlim = (-1, 6)
ps.figa(t,
px,
colour,
label,
xlim=xlim,
title=string,
linestyle=lstyle,
xlabel='t$\\ /\\ $h',
ylabel='c$\\ / \\ $ a.u.',
label=True,
path='../../graphics/discreet{}.png'.format(kwargs.get('mode',
'')),
DPI=500)
def discrTalk(py, pt, **kwargs):
mode = kwargs.get('mode', 'limit')
(m6, m7, m12, m1, n1) = prc.evmode(mode)
t = [pt, pt, pt, pt]
xlim = (-1, 6)
lstyle = ['--', '-', (0, (1, 1))]
xlab = 'Time'
ylab = 'Activity'
MAX7 = np.amax(py[7])
TH7 = m7 / MAX7
plt.style.use('seaborn-paper')
seaborn.set_context("talk")
fig, ax = plt.subplots(1, 1)
px3 = [ps.hline(TH7, pt), prc.discr(py[7], m7), prc.norm(py[7])]
colour3 = [c.plum, c.gold, c.orange]
for i, j in enumerate(px3):
ax.plot(t[i] - 101, j, c=colour3[i], linestyle=lstyle[i])
ax.set_title('A20')
ax.set_xlim(xlim)
ax.set_yticks([])
ax.set_xticks([])
ax.set_xlabel(xlab)
ax.set_ylabel(ylab)
ax.yaxis.set_zorder(3)
fig.tight_layout()
plt.savefig('../../graphics/discrTalk{}{}.png'.format(
kwargs.get('strg', ''), mode),
dpi=500)
plt.close()
def discreetmedian(py, pt, *string):
t = [pt, pt, pt, pt]
px = [
prc.discr(py[6], np.median(py[6])),
prc.discr(py[1], np.median(py[1])),
prc.discr(py[7], np.median(py[7])),
prc.discr(py[12], np.median(py[12]))
]
colour = ['navy', c.blood, c.darkorange, c.green]
label = ['NF$\kappa$B', 'IKKa', 'A20', 'NF$\kappa$B:I$\kappa$B']
lstyle = ['-', '-', '-', '-']
xlim = (-1, 6)
ps.figa(t,
px,
colour,
label,
xlim=xlim,
title=string,
linestyle=lstyle,
xlabel='t$\\ /\\ $h',
ylabel='c$\\ / \\ $ a.u.',
label=True,
path='../../graphics/discreetmedian.png',
DPI=500)
def discr(py,**kwargs):
mode=kwargs.get('mode','limit')
y=[]
for i in range(0,len(py)):
if mode=='limit':
if i==1:
y.append(np.array(prc.discr(py[i],mod.limit1(i),mod.limitKO(i))))
else:
y.append(np.array(prc.discr(py[i],mod.limit1(i))))
elif mode=='mean':
if i==1:
y.append(np.array(prc.discr(py[i],mod.meanpy(i)/2,mod.meanpy(i))))
else:
y.append(np.array(prc.discr(py[i],mod.meanpy(i))))
elif mode =='half':
if i==1:
y.append(np.array(prc.discr(py[i],(mod.limit0(i)+mod.limit1(i))/2,(mod.limit0(i)+mod.limitKO(i))/2)))
else:
y.append(np.array(prc.discr(py[i],(mod.limit0(i)+mod.limit1(i))/2)))
elif mode=='hmean':
if i==1:
y.append(np.array(prc.discr(py[i],(mod.limit0(i)+mod.meanpy(i))/2,(mod.limit0(i)+mod.meanKO(i))/2)))
else:
y.append(np.array(prc.discr(py[i],(mod.limit0(i)+mod.meanpy(i))/2)))
elif mode=='custom':
if i==1:
y.append(np.array(prc.discr(py[i],(mod.limit0(i)+mod.limit1(i))/2,mod.mean24(i))))
else:
y.append(np.array(prc.discr(py[i],mod.mean24(i))))
elif mode=='custom2':
if i==1:
y.append(np.array(prc.discr(py[i],(mod.limit0(1)+mod.limit1(1))/2,mod.mean24(1))))
elif i==7:
y.append(np.array(prc.discr(py[i],((mod.limit0(7)+mod.limit1(7))/2))))
else:
y.append(np.array(prc.discr(py[i],mod.mean24(i))))
elif mode=='custom3':#median, hlim
if i==1:
y.append(np.array(prc.discr(py[i],(mod.limit0(i)+mod.limit1(i))/2,mod.median(i))))
else:
y.append(np.array(prc.discr(py[i],mod.median(i))))
y=np.stack(y)
return y
def discrnor(py, pt, **kwargs):
mode = kwargs.get('mode', 'limit')
(m6, m7, m12, m1, n1) = prc.evmode(mode)
t = [pt, pt, pt, pt]
xlim = (-1, 6)
label = ['Normalisation', 'Discretisation', '$\\vartheta$']
lstyle = ['-', '--', '-.', '-.']
tick = [0, 0.5, 1]
mtick = [0.25, 0.75]
xlab = '$t$ in h'
ylab = '$c$ in nM'
ylab2 = 'Activity'
c1 = c.plum
c2 = c.deeppink
MAX6 = np.amax(py[6])
TH6 = m6 / MAX6
MAX12 = np.amax(py[12])
TH12 = m12 / MAX12
MAX7 = np.amax(py[7])
TH7 = m7 / MAX7
MAX1 = np.amax(py[1])
TH1_1 = m1 / MAX1
TH1_2 = n1 / MAX1
thresh1 = Line2D([0], [0], color=c1, lw=1, linestyle='-.')
thresh2 = Line2D([0], [0], color=c2, lw=1, linestyle=':')
l1 = Line2D([0], [0], color='black', lw=1, linestyle='-')
l2 = Line2D([0], [0], color='black', lw=1, linestyle='--')
plt.style.use('seaborn-paper')
fig, ((ax1, ax2), (ax3, ax4)) = plt.subplots(2, 2)
px1 = [prc.norm(py[6]), prc.discr(py[6], m6), ps.hline(TH6, pt)]
colour1 = ['navy', c.dodgerblue, c1]
for i, j in enumerate(px1):
ax3.plot(t[i] - 101, j, c=colour1[i], linestyle=lstyle[i])
ax3.set_title('NF$\kappa$B')
ax3.set_xlim(xlim)
ax3.set_yticks(tick)
ax3.set_yticks(TH6, minor=True)
ax3.set_yticklabels([
0,
np.around(MAX6 * 500, decimals=1),
np.around(MAX6 * 1000, decimals=1)
])
ax3.set_yticklabels([np.around(MAX6 * TH6[0] * 1000, decimals=1)],
minor=True)
ax3.set_xlabel(xlab)
ax3.set_ylabel(ylab)
ax32 = ax3.twinx()
ax32.yaxis.tick_right()
NUL = ax32.transData.inverted().transform(ax3.transData.transform(
(0, 0)))[1]
ONE = ax32.transData.inverted().transform(ax3.transData.transform(
(1, 1)))[1]
ax32.set_yticks([NUL, ONE])
ax32.set_yticklabels([0, 1])
ax32.set_ylabel(ylab2)
px2 = [prc.norm(py[12]), prc.discr(py[12], m12), ps.hline(TH12, pt)]
colour2 = [c.green, c.lime, c1]
for i, j in enumerate(px2):
ax2.plot(t[i] - 101, j, c=colour2[i], linestyle=lstyle[i])
ax2.set_title('I$\kappa$B')
ax2.set_xlim(xlim)
ax2.set_yticks(tick)
ax2.set_yticks(TH12, minor=True)
ax2.set_yticklabels([
0,
np.around(MAX12 * 500, decimals=1),
np.around(MAX12 * 1000, decimals=1)
])
ax2.set_yticklabels([np.around(MAX12 * TH12[0] * 1000, decimals=1)],
minor=True)
ax2.set_xlabel(xlab)
ax2.set_ylabel(ylab)
ax22 = ax2.twinx()
ax22.yaxis.tick_right()
NUL = ax22.transData.inverted().transform(ax2.transData.transform(
(0, 0)))[1]
ONE = ax22.transData.inverted().transform(ax2.transData.transform(
(1, 1)))[1]
ax22.set_yticks([NUL, ONE])
ax22.set_yticklabels([0, 1])
ax22.set_ylabel(ylab2)
#lstyle[-2]=':'
px3 = [prc.norm(py[7]), prc.discr(py[7], m7), ps.hline(TH7, pt)]
colour3 = [c.darkorange, c.gold, c1]
for i, j in enumerate(px3):
ax4.plot(t[i] - 101, j, c=colour3[i], linestyle=lstyle[i])
ax4.set_title('A20')
ax4.set_xlim(xlim)
ax4.set_yticks(tick)
ax4.set_yticks(TH7, minor=True)
ax4.set_yticklabels([
0,
np.around(MAX7 * 500, decimals=1),
np.around(MAX7 * 1000, decimals=1)
])
ax4.set_yticklabels([np.around(MAX7 * TH7[0] * 1000, decimals=1)],
minor=True)
ax4.yaxis.get_ticklabels(minor=True)[0].set_verticalalignment('top')
ax4.yaxis.get_ticklabels()[1].set_verticalalignment('baseline')
ax4.set_xlabel(xlab)
ax4.set_ylabel(ylab)
ax42 = ax4.twinx()
ax42.yaxis.tick_right()
NUL = ax42.transData.inverted().transform(ax4.transData.transform(
(0, 0)))[1]
ONE = ax42.transData.inverted().transform(ax4.transData.transform(
(1, 1)))[1]
ax42.set_yticks([NUL, ONE])
ax42.set_yticklabels([0, 1])
ax42.set_ylabel(ylab2)
px4 = [
prc.norm(py[1]),
prc.discr(py[1], m1, n1),
ps.hline(TH1_1, pt),
ps.hline(TH1_2, pt)
]
colour4 = [c.blood, 'r', c2, c1]
for i, j in enumerate(px4):
ax1.plot(t[i] - 101, j, c=colour4[i], linestyle=lstyle[i])
ax1.set_title('IKK')
ax1.set_xlim(xlim)
ax1.set_yticks(tick)
ax1.set_yticks(np.append(TH1_1, TH1_2), minor=True)
ax1.set_yticklabels([
'',
np.around(MAX1 * 500, decimals=1),
np.around(MAX1 * 1000, decimals=1)
])
ax1.set_yticklabels([
np.around(MAX1 * TH1_1[0] * 1000, decimals=1),
np.around(MAX1 * TH1_2[0] * 1000, decimals=1)
],
minor=True)
ax1.set_xlabel(xlab)
ax1.set_ylabel(ylab)
ax1.yaxis.get_ticklabels(minor=True)[0].set_verticalalignment('top')
ax1.yaxis.get_ticklabels(minor=True)[1].set_verticalalignment('baseline')
ax12 = ax1.twinx()
ax12.yaxis.tick_right()
NUL = ax12.transData.inverted().transform(ax1.transData.transform(
(0, 0)))[1]
HALF = ax12.transData.inverted().transform(
ax1.transData.transform((0, 0.5)))[1]
ONE = ax12.transData.inverted().transform(ax1.transData.transform(
(1, 1)))[1]
ax12.set_yticks([NUL, HALF, ONE])
ax12.set_yticklabels([0, 1, 2])
ax12.set_ylabel(ylab2)
handles = [l1, l2, thresh1, thresh2]
labels = [
'Simulation', 'Discretisation', '$\\vartheta_\mathrm{mean}$',
'$\\vartheta_\mathrm{half}$'
]
for ax in fig.axes:
plt.setp(ax.get_yticklabels(which='both'), fontsize=7)
plt.setp(ax.get_xticklabels(which='both'), fontsize=7)
ax.tick_params(direction='in')
ax.yaxis.set_zorder(3)
fig.legend(handles,
labels,
loc=(.4, 0.47),
fontsize=6,
framealpha=1,
prop={'size': 7},
edgecolor='k',
ncol=2)
fig.tight_layout()
plt.savefig('../../graphics/discrnor{}{}.png'.format(
kwargs.get('strg', ''), mode),
dpi=500)
plt.close()
def discr(py, pt, **kwargs):
mode = kwargs.get('mode', 'limit')
(m6, m7, m12, m1, n1) = prc.evmode(mode)
t = [pt, pt, pt, pt]
xlim = (-1, 6)
label = ['Simulation', 'Discretisation', '$\\vartheta$']
lstyle = ['-', '--', ':']
tick = [0, 0.5, 1]
xlab = '$t$ in h'
ylab = '$c$ in nM'
ylab2 = 'Activity'
MAX7 = np.amax(py[7])
TH7 = m7 / MAX7
plt.style.use('seaborn-paper')
fig, ax = plt.subplots(1, 1)
fig.set_size_inches(3.2, 2.2)
px3 = [prc.norm(py[7]), prc.discr(py[7], m7), ps.hline(TH7, pt)]
colour3 = [c.darkorange, c.gold, c.deeppink]
for i, j in enumerate(px3):
ax.plot(t[i] - 101,
j,
c=colour3[i],
linestyle=lstyle[i],
label=label[i])
ax.set_title('A20')
ax.set_xlim(xlim)
ax.set_yticks(tick)
ax.set_yticks(TH7, minor=True)
ax.set_yticklabels([
0,
np.around(MAX7 * 500, decimals=1),
np.around(MAX7 * 1000, decimals=1)
])
ax.set_yticklabels([np.around(MAX7 * TH7[0] * 1000, decimals=1)],
minor=True)
ax.yaxis.get_ticklabels(minor=True)[0].set_verticalalignment('top')
ax.yaxis.get_ticklabels()[1].set_verticalalignment('baseline')
ax.set_xlabel(xlab)
ax.set_ylabel(ylab)
ax.legend(loc=(0.5, 0.1),
prop={'size': 6},
framealpha=0,
fontsize=3,
edgecolor=None)
ax2 = ax.twinx()
ax2.yaxis.tick_right()
NUL = ax2.transData.inverted().transform(ax.transData.transform((0, 0)))[1]
ONE = ax2.transData.inverted().transform(ax.transData.transform((1, 1)))[1]
ax2.set_yticks([NUL, ONE])
ax2.set_yticklabels([0, 1])
ax2.set_ylabel(ylab2)
for ax in fig.axes:
plt.setp(ax.get_yticklabels(which='both'), fontsize=7)
plt.setp(ax.get_xticklabels(which='both'), fontsize=7)
ax.tick_params(direction='in')
ax.yaxis.set_zorder(3)
fig.tight_layout()
plt.savefig('../../graphics/discr{}{}.png'.format(kwargs.get('strg', ''),
mode),
dpi=500)
plt.close()
def discrnorTalk(py, pt, **kwargs):
mode = kwargs.get('mode', 'limit')
(m6, m7, m12, m1, n1) = prc.evmode(mode)
t = [pt, pt, pt, pt]
xlim = (-1, 6)
lstyle = ['--', '-', (0, (1, 1))]
width = [1, 2, 2]
tick = [0, 0.5, 1]
mtick = [0.25, 0.75]
xlab = 'Time'
ylab = 'Activity'
c1 = c.plum
c2 = c.deeppink
MAX6 = np.amax(py[6])
TH6 = m6 / MAX6
MAX12 = np.amax(py[12])
TH12 = m12 / MAX12
MAX7 = np.amax(py[7])
TH7 = m7 / MAX7
MAX1 = np.amax(py[1])
TH1_1 = m1 / MAX1
TH1_2 = n1 / MAX1
plt.style.use('seaborn-paper')
seaborn.set_context("talk")
fig, ((ax1, ax2), (ax3, ax4)) = plt.subplots(2, 2)
px1 = [ps.hline(TH6, pt), prc.discr(py[6], m6), prc.norm(py[6])]
colour1 = [c1, c.dodgerblue, 'navy']
for i, j in enumerate(px1):
ax3.plot(t[i] - 101,
j,
c=colour1[i],
linestyle=lstyle[i],
linewidth=width[i])
ax3.set_title('NF$\kappa$B')
ax3.set_xlim(xlim)
ax3.set_yticks([])
ax3.set_xticks([])
ax3.set_xlabel(xlab)
ax3.set_ylabel(ylab)
px2 = [ps.hline(TH12, pt), prc.discr(py[12], m12), prc.norm(py[12])]
colour2 = [c1, c.lime, c.green]
for i, j in enumerate(px2):
ax2.plot(t[i] - 101,
j,
c=colour2[i],
linestyle=lstyle[i],
linewidth=width[i])
ax2.set_title('I$\kappa$B')
ax2.set_xlim(xlim)
ax2.set_yticks([])
ax2.set_xticks([])
ax2.set_xlabel(xlab)
ax2.set_ylabel(ylab)
px3 = [ps.hline(TH7, pt), prc.discr(py[7], m7), prc.norm(py[7])]
colour3 = [c1, c.gold, c.darkorange]
if mode == 'custom2':
colour3[0] = c2
lstyle[0] = '-.'
for i, j in enumerate(px3):
ax4.plot(t[i] - 101,
j,
c=colour3[i],
linestyle=lstyle[i],
linewidth=width[i])
ax4.set_title('A20')
ax4.set_xlim(xlim)
ax4.set_yticks([])
ax4.set_xticks([])
ax4.set_xlabel(xlab)
ax4.set_ylabel(ylab)
if mode == 'custom2':
lstyle.insert(1, '-.')
else:
lstyle.insert(0, '-.')
width.insert(0, 1)
px4 = [
ps.hline(TH1_1, pt),
ps.hline(TH1_2, pt),
prc.discr(py[1], m1, n1),
prc.norm(py[1])
]
colour4 = [c2, c1, 'r', c.blood]
for i, j in enumerate(px4):
ax1.plot(t[i] - 101,
j,
c=colour4[i],
linestyle=lstyle[i],
linewidth=width[i])
ax1.set_title('IKK')
ax1.set_xlim(xlim)
ax1.set_yticks([])
ax1.set_xticks([])
ax1.set_xlabel(xlab)
ax1.set_ylabel(ylab)
fig.tight_layout()
plt.savefig('../../graphics/discrnorTalk{}{}.png'.format(
kwargs.get('strg', ''), mode),
dpi=500)
plt.close()