fig, ax = plt.subplots(ncols=3, nrows=2)
fig.suptitle("Chro " + str(chro))
for r, rep in enumerate(reps):
FULL_STRUC_STRING = "Generated_Structures/cardio_full_rep_" + str(
rep
) + "_eta_1000_alpha_0.6_lr_0.0001_epoch_400_res_1_step_15_chro_" + str(
chro) + ".npy"
MIS_STRUC_STRING = "Generated_Structures/cardio_missing_2_rep_" + str(
rep
) + "_eta_1000_alpha_0.6_lr_0.0001_epoch_400_res_1_step_15_chro_" + str(
chro) + ".npy"
CONTACT_STRING = "Real_Data/Cardiomyocyte/RUES2/By_Chros/*_MES_Rep" + str(
rep) + "_500KB_" + str(chro)
CONTACT_STRING = glob.glob(CONTACT_STRING)[0]
mat_contacts[r] = ut.loadConstraintAsMat(CONTACT_STRING, res=1)
mat_mis_struc[r] = ut.loadStrucAtTimeAsMat(MIS_STRUC_STRING, time)
mat_full_struc[r] = ut.loadStrucAtTimeAsMat(FULL_STRUC_STRING, time)
for r, rep in enumerate(reps):
ax[r, 0].set_ylabel("Rep " + str(rep))
ax[r, 0].imshow(np.clip(mat_contacts[r], 0, 30), cmap="Reds")
ax[r, 1].imshow(np.clip(mat_mis_struc[r], 0, 10), cmap="Reds")
ax[r, 2].imshow(np.clip(mat_full_struc[r], 0, 10), cmap="Reds")
ax[1, 0].set_xlabel("Hi-C")
ax[1, 1].set_xlabel("Recon")
ax[1, 2].set_xlabel("Interp")
print("CHRO" + str(chro))
print(spearmanr(mat_contacts[0], mat_contacts[0], axis=None))
print(spearmanr(mat_contacts[0], mat_full_struc[0], axis=None))
print(spearmanr(mat_contacts[0], mat_mis_struc[0], axis=None))
print(spearmanr(mat_contacts[0], mat_contacts[1], axis=None))
chro_full_spears = np.load("Fig_Scripts/iPSC_SPC_ful.npy", allow_pickle=True).item()
pdb.set_trace()
for chro in CHROS:
if chro in chro_mis_spears.keys():
continue
for r, rep in enumerate(reps):
for day in DAY_LABELS:
CONTACT_STRING = "Real_Data/iPluripotent/day_"+day+"_rep_"+str(rep)+"_chro_"+str(chro)
print(CONTACT_STRING)
mat_contacts[r, day] = ut.loadConstraintAsMat(CONTACT_STRING)
for m, mis in enumerate(MISS):
MIS_STRUC_STRING = "Generated_Structures/ipsc_missing_"+str(mis)+"_rep_"+str(rep)+"_eta_"+str(eta)+"_alpha_"+str(alpha)+"_lr_"+str(lr)+"_epoch_"+str(epoch)+"_res_"+str(res)+"_step_"+str(step)+"_chro_"+str(chro)+".npy"
FULL_STRUC_STRING = "Generated_Structures/ipsc_full_rep_"+str(rep)+"_eta_"+str(eta)+"_alpha_"+str(alpha)+"_lr_" +str(lr)+"_epoch_"+str(epoch)+"_res_"+str(res)+"_step_"+str(step)+"_chro_"+str(chro)+".npy"
print(MIS_STRUC_STRING)
mat_mis_struc[r, mis] = ut.loadStrucAtTimeAsMat(MIS_STRUC_STRING, MIS_TIMES[m])
mat_full_struc[r, mis] = ut.loadStrucAtTimeAsMat(FULL_STRUC_STRING, MIS_TIMES[m])
mis_spears = np.zeros((len(reps), len(MISS), len(DAY_LABELS)))
full_spears = np.zeros((len(reps), len(MISS), len(DAY_LABELS)))
for r, rep in enumerate(reps):
for m, mis in enumerate(MISS):
for d, day in enumerate(DAY_LABELS):
mis_spears[r,m,d] = spearmanr(mat_mis_struc[0,mis], mat_contacts[0,day], axis=None)[0]
full_spears[r,m,d] = spearmanr(mat_full_struc[0,mis], mat_contacts[0,day], axis=None)[0]
chro_mis_spears[chro]=mis_spears
chro_full_spears[chro]=full_spears
pdb.set_trace()
np.save("Fig_Scripts/iPSC_SPC_mis",chro_mis_spears)
epoch = 400
reps = [1, 2]
mat_contacts = {}
mat_mis_struc = {}
mat_full_struc = {}
rep = 1
FULL_STRUC_STRING = "Generated_Structures/ipsc_full_rep_" + str(
rep) + "_eta_" + str(eta) + "_alpha_" + str(alpha) + "_lr_" + str(lr)
FULL_STRUC_STRING += "_epoch_" + str(epoch) + "_res_" + str(
res) + "_step_" + str(step) + "_chro_" + str(chro) + ".npy"
for t, (time, day) in enumerate(
zip([0, 4, 8, 12, 16, 20], ['B', 'D2', 'D4', 'D6', 'D8', 'ES'])):
mat_full_struc[t] = ut.loadStrucAtTimeAsMat(FULL_STRUC_STRING, time)
CONTACT_STRING = "Real_Data/iPluripotent/day_" + str(
day) + "_rep_" + str(rep) + "_chro_" + str(chro)
mat_contacts[t] = ut.loadConstraintAsMat(CONTACT_STRING)
for d, day in enumerate(['B', 'D2', 'D4', 'D6', 'D8', 'ES']):
for t, time in enumerate([0, 4, 8, 12, 16, 20]):
print(
str(day) + "/" + str(time) + ":" + str(
spearmanr(mat_full_struc[t], mat_contacts[d], axis=None)
[0]))
fig, ax = plt.subplots(2, 6, gridspec_kw={'wspace': 0.0, 'hspace': 0.0})
for t, time in enumerate([0, 4, 8, 12, 16, 20]):
ax[0, t].imshow(np.clip(mat_full_struc[t], 0, 10), cmap="PuBuGn")
ax[1, t].imshow(np.clip(mat_contacts[t], 0, 30), cmap="YlOrRd")
import pdb
from scipy.stats import pearsonr
from scipy.stats import spearmanr
import numpy as np
import matplotlib.pyplot as plt
from Utils import util as ut
fig, ax = plt.subplots(6, 6)
for day, time in zip([0, 1, 2, 3, 4, 5], [0, 4, 8, 12, 16, 20]):
real1 = 1 / ut.loadConstraintAsMat(
"Synthetic_Data/Synthetic_Contact_Maps/struc1_" + str(day) + ".txt",
res=100000)
real2 = 1 / ut.loadConstraintAsMat(
"Synthetic_Data/Synthetic_Contact_Maps/struc2_" + str(day) + ".txt",
res=100000)
full1 = 1 / ut.loadStrucAtTimeAsMat(
"Generated_Structures/synthetic_full_rep_1_eta_10_alpha_1.0_lr_0.01_epoch_1000_res_100000_step_21_chro_all.npy",
time)
full2 = 1 / ut.loadStrucAtTimeAsMat(
"Generated_Structures/synthetic_full_rep_2_eta_10_alpha_1.0_lr_0.01_epoch_1000_res_100000_step_21_chro_all.npy",
time)
if day == 0 or day == 5:
struc1 = 1 / ut.loadStrucAtTimeAsMat(
"Generated_Structures/synthetic_full_rep_1_eta_10_alpha_1.0_lr_0.01_epoch_1000_res_100000_step_21_chro_all.npy",
time)
struc2 = 1 / ut.loadStrucAtTimeAsMat(
"Generated_Structures/synthetic_full_rep_2_eta_10_alpha_1.0_lr_0.01_epoch_1000_res_100000_step_21_chro_all.npy",
time)
else:
struc1 = 1 / ut.loadStrucAtTimeAsMat(
"Generated_Structures/synthetic_missing_" + str(day) +
"_rep_1_eta_10_alpha_1.0_lr_0.01_epoch_1000_res_100000_step_21_chro_all.npy",