import sys
import numpy as np
import numpy.ma as ma
import matplotlib.pyplot as plt
import pdb
sys.path.insert(0, "../")
from Utils import util as ut
chro = "13"
struc = np.load(
"../Generated_Structures/ipsc_missing_2_rep_1_eta_1000_alpha_0.6_lr_0.0001_epoch_400_res_50000_step_21_chro_"
+ str(chro) + ".npy")
real_map = ut.loadConstraintAsMat(
"../Real_Data/iPluripotent/day_D2_rep_1_chro_" + str(chro))
struc_map = ut.struc2contacts(struc[4])
struc_map = np.clip(struc_map, 0, 10)
real_map = np.clip(real_map, 0, 30)
real_pear = ma.corrcoef(ma.masked_invalid(real_map))
struc_pear = ma.corrcoef(ma.masked_invalid(struc_map))
pca_real = PCA(n_components=1)
pca_struc = PCA(n_components=1)
ab_real = pca_real.fit_transform(real_pear)
ab_struc = pca_struc.fit_transform(struc_pear)
real_vec = np.squeeze(ab_real)
struc_vec = np.squeeze(ab_struc)
fig, ax = plt.subplots(3, 2)
ax[0, 0].imshow(np.clip(struc_map, 0, 10), cmap="Reds")
ax[0, 1].imshow(np.clip(real_map, 0, 30), cmap="Reds")
for chro in chros:
for missing, missing_time in zip(missings, missing_times):
for day in days:
print(str(chro), str(day), str(missing))
#chro = 3
#day = 'D2'
#missing = 2
#missing_time = 4
real_map = ut.loadConstraintAsMat(
"../Real_Data/iPluripotent/day_" + str(day) + "_rep_1_chro_" +
str(chro))
struc = np.load(
"../Generated_Structures/ipsc_missing_" + str(missing) +
"_rep_1_eta_1000_alpha_0.6_lr_0.0001_epoch_400_res_50000_step_21_chro_"
+ str(chro) + ".npy")
struc_map = ut.struc2contacts(struc[missing_time])
#shrink to 100kb
real_map_torch = torch.from_numpy(real_map)
real_map_torch = real_map_torch.unsqueeze(0).unsqueeze(0)
resized_real_map = torch.nn.functional.avg_pool2d(real_map_torch,
kernel_size=2)
resized_real_map = resized_real_map.squeeze()
real_map = resized_real_map.numpy()
struc_map_torch = torch.from_numpy(struc_map)
struc_map_torch = struc_map_torch.unsqueeze(0).unsqueeze(0)
resized_struc_map = torch.nn.functional.avg_pool2d(struc_map_torch,
kernel_size=2)
resized_struc_map = resized_struc_map.squeeze()
struc_map = resized_struc_map.numpy()
import numpy as np
import matplotlib.pyplot as plt
import numpy.ma as ma
import pdb
from sklearn.decomposition import PCA
import sys
sys.path.insert(0, "../")
import matplotlib.pyplot as plt
from Utils import util as ut
import sys
struc_file = sys.argv[1]
out_file = sys.argv[2]
start_time = time.time()
struc = np.load(struc_file)
AB_VEC = np.zeros((struc.shape[0], struc.shape[1]))
for i, ti in enumerate(range(0, struc.shape[0])):
print("(" + str(i) + "/" + str(struc.shape[0]) + ")" + ":" +
str(time.time() - start_time))
struc_snap = struc[ti]
contact = ut.struc2contacts(struc_snap)
contact = np.clip(contact, 0, 10)
pear = ma.corrcoef(ma.masked_invalid(contact))
pca = PCA(n_components=1)
AB = pca.fit_transform(pear)
AB_VEC[i] = np.squeeze(AB)
np.save(out_file, AB_VEC)
for chro in chros:
for day in days:
print(str(chro),str(day))
real_map[day] = ut.loadConstraintAsMat("../Real_Data/iPluripotent/day_"+str(day)+"_rep_1_chro_"+str(chro))
real_map_torch = torch.from_numpy(real_map[day])
real_map_torch = real_map_torch.unsqueeze(0).unsqueeze(0)
resized_real_map = torch.nn.functional.avg_pool2d(real_map_torch, kernel_size=2)
resized_real_map = resized_real_map.squeeze()
real_map[day] = resized_real_map.numpy()
struc = np.load("../Generated_Structures/ipsc_full_rep_1_eta_1000_alpha_0.6_lr_0.0001_epoch_400_res_50000_step_21_chro_"+str(chro)+".npy")
for struc_time in struc_times:
print(str(chro), str(struc_time))
struc_map[struc_time] = ut.struc2contacts(struc[struc_time])
struc_map_torch = torch.from_numpy(struc_map[struc_time])
struc_map_torch = struc_map_torch.unsqueeze(0).unsqueeze(0)
resized_struc_map = torch.nn.functional.avg_pool2d(struc_map_torch, kernel_size=2)
resized_struc_map = resized_struc_map.squeeze()
struc_map[struc_time] = resized_struc_map.numpy()
#impute time
not_valid = []
for day in days:
not_valid.extend(np.where(np.diagonal(real_map[day])==0)[0])
for day in days:
real_map[day] = np.delete(np.delete(real_map[day], not_valid, axis=0), not_valid, axis=1)
for struc_time in struc_times:
struc_map[struc_time] = np.delete(np.delete(struc_map[struc_time], not_valid, axis=0), not_valid, axis=1)
for day in days:
import matplotlib.pyplot as plt import numpy as np import pdb import sys from Utils import util as ut struc_name = sys.argv[1] time = int(sys.argv[2]) ref_map = sys.argv[3] res = int(sys.argv[4]) struc = np.load(struc_name) mat = ut.struc2contacts(struc[time]) x = np.loadtxt(ref_map) row = x[:, 0].astype(int) col = x[:, 1].astype(int) ifs = x[:, 2].astype(float) row = (row / res).astype(int) col = (col / res).astype(int) real_mat = ut.constraints2mats(row, col, ifs) pdb.set_trace() plt.imshow(np.log(real_mat), cmap="Reds") plt.show()