def compute_periods(cell='NIH3T3'):
"""
Given a cell condition, compute and plot a boxplot with all periods
distributions for all temperature conditions, in dividing and non-dividing
conditions.
Parameters
----------
cell : string
Cell condition.
"""
if cell == 'NIH3T3':
path = "../Data/NIH3T3.ALL.2017-04-04/ALL_TRACES_INFORMATION.p"
else:
path = "../Data/U2OS-2017-03-20/ALL_TRACES_INFORMATION_march_2017.p"
nb_traces = 10000000
t_T = (34, 37, 40)
l_T_full = []
for T in t_T:
### COMPUTE LIST CIRCADIAN PERIOD ###
division = True
dataClass = LoadData(path, nb_traces, temperature=T, division=division)
(ll_area, ll_signal, ll_peak, ll_cell_cycle_start,
ll_mitosis_start) = dataClass.filter_data()
l_T = []
for l_peak in ll_peak:
l_idx_peak = [idx for idx, i in enumerate(l_peak) if i == 1]
for t_peak_1, t_peak_2 in zip(l_idx_peak[:-1], l_idx_peak[1:]):
#print(t_peak_1, t_peak_2)
l_T.append((t_peak_2 - t_peak_1) / 2)
l_T_full.append(l_T)
division = False
dataClass = LoadData(path, nb_traces, temperature=T, division=division)
(ll_area, ll_signal, ll_peak, ll_cell_cycle_start,
ll_mitosis_start) = dataClass.filter_data()
l_T = []
for l_peak in ll_peak:
l_idx_peak = [idx for idx, i in enumerate(l_peak) if i == 1]
for t_peak_1, t_peak_2 in zip(l_idx_peak[:-1], l_idx_peak[1:]):
#print(t_peak_1, t_peak_2)
l_T.append((t_peak_2 - t_peak_1) / 2)
l_T_full.append(l_T)
### COMPUTE LIST CELL-CYCLE PERIOD ###
division = True
ll_idx_cell_cycle_start = []
dataClass = LoadData(path, nb_traces, temperature=T, division=division)
(ll_area, ll_signal, ll_peak, ll_cell_cycle_start,
ll_mitosis_start) = dataClass.filter_data()
zp = zip(enumerate(ll_mitosis_start), ll_cell_cycle_start)
for (idx, l_mitosis_start), l_cell_cycle_start in zp:
l_idx_mitosis_start = [idx for idx, i in \
enumerate(l_mitosis_start) if i==1]
l_idx_cell_cycle_start = [idx for idx, i in \
enumerate(l_cell_cycle_start) if i==1]
ll_idx_cell_cycle_start.append(l_idx_cell_cycle_start)
l_T2 = []
for l_idx_cell_cycle_start in ll_idx_cell_cycle_start:
for t_start_1, t_start_2 in zip(l_idx_cell_cycle_start[:-1],
l_idx_cell_cycle_start[1:]):
#print(t_peak_1, t_peak_2)
l_T2.append((t_start_2 - t_start_1) / 2)
l_T_full.append(l_T2)
#plt.style.use('default')
l_label_full = [
r'$T_\theta^D$,34°C', r'$T_\theta^{ND}$,34°C', r'$T_\phi^D$,34°C',
r'$T_\theta^D$,37°C', r'$T_\theta^{ND}$,37°C', r'$T_\phi^D$,37°C',
r'$T_\theta^D$,40°C', r'$T_\theta^{ND}$,40°C', r'$T_\phi^D$,40°C'
]
# Create a figure instance
fig = plt.figure(1, figsize=(10, 5))
# Create an axes instance
ax = fig.add_subplot(111)
## add patch_artist=True option to ax.boxplot()
## to get fill color
bp = ax.boxplot(l_T_full, showmeans=False, patch_artist=True)
#ax.axhline(22, ls = '--',color = 'yellow', label = '22h')
#ax.axhline(24, ls = '--', color = 'orange', label = '24h')
ax.legend()
## change outline color, fill color and linewidth of the boxes
for i, box in enumerate(bp['boxes']):
# change outline color
box.set(color='#7570b3', linewidth=2)
if (i + 1) % 3 == 0:
# change fill color
box.set(facecolor='#1b9e77')
## change color and linewidth of the whiskers
for whisker in bp['whiskers']:
whisker.set(color='#7570b3', linewidth=2)
## change color and linewidth of the caps
for cap in bp['caps']:
cap.set(color='#7570b3', linewidth=2)
## change color and linewidth of the medians
for median in bp['medians']:
median.set(color='#b2df8a', linewidth=2)
## change the style of fliers and their fill
for flier in bp['fliers']:
flier.set(marker='o', color='#e7298a', alpha=0.5)
ax.set_xticklabels(l_label_full)
ax.get_xaxis().tick_bottom()
ax.get_yaxis().tick_left()
plt.ylabel('Hours')
if not os.path.exists("../Results/RawData"):
os.makedirs("../Results/RawData")
fig.savefig('../Results/RawData/Periods.pdf', bbox_inches='tight')
fig.show()
plt.close()
