import os
import numpy as np
import sys
sys.path.append("..")
import data_tools as dt
import plotting as plot
os.system(
"python ../multimds.py -P 0.1 -w 0 ctrl_Scer_13_32kb.bed galactose_Scer_13_32kb.bed"
)
struct1 = dt.structure_from_file("ctrl_Suva_13_32kb_structure.tsv")
struct2 = dt.structure_from_file("galactose_Suva_13_32kb_structure.tsv")
colors = np.zeros_like(struct1.getPoints(), dtype=int)
colors[struct1.get_rel_index(852000)] = 1
plot.plot_structures_interactive((struct1, struct2), (colors, colors))
import sys
sys.path.append("..")
import data_tools as dt
import numpy as np
import plotting as plot
cell_type = sys.argv[1]
res_kb = int(sys.argv[2])
struct = dt.structure_from_file("{}_21_{}kb_structure.tsv".format(
cell_type, res_kb))
#truncate
start = 45000000
index = struct.chrom.getAbsoluteIndex(start)
struct.points = struct.points[index:len(struct.points)]
struct.chrom.minPos = start
for i in range(len(struct.points)):
if struct.points[i] != 0:
struct.points[i].absolute_index -= index
struct.set_rel_indices()
colors = np.zeros_like(struct.getPoints(), dtype=int)
colors[struct.get_rel_index(46900000):struct.get_rel_index(46950000)] = 2
colors[struct.get_rel_index(47475000)] = 1
plot.plot_structure_interactive(struct, colors, colormap="brg")
prefix2 = os.path.basename(path2.split(".")[0])
n = 10
all_r_sq = []
ps = np.arange(0, 0.1, 0.01)
for p in ps:
all_changes = []
for i in range(n):
print(i)
os.system("python ../multimds.py -P {} --full {} {}".format(
p, path1, path2))
structure1 = dt.structure_from_file("{}_structure.tsv".format(
os.path.basename(prefix1)))
structure2 = dt.structure_from_file("{}_structure.tsv".format(
os.path.basename(prefix2)))
if p == 0:
r, t = la.getTransformation(structure1, structure2)
structure1.transform(r, t)
all_changes.append(
np.array([
la.calcDistance(coord1, coord2) for coord1, coord2 in zip(
structure1.getCoords(), structure2.getCoords())
]))
r_sq = []
for i in range(n):
return misc.pearson(dists1, dists2)
#labels = ("Chromosome3D", "mMDS", "miniMDS", "MOGEN", "HSA", "ChromSDE")
labels = ("mMDS", "miniMDS", "MOGEN", "HSA")
n = len(labels)
rs = np.zeros(n)
#Chromosome3D
#coords1 = np.loadtxt("Chromosome3D/output_models/chr22_10kb_rep1/rep1_coords.tsv")
#coords2 = np.loadtxt("Chromosome3D/output_models/chr22_10kb_rep1/rep2_coords.tsv")
#rs[0] = rep_correlation(coords1, coords2)
#mMDS
coords1 = dt.structure_from_file(
"hic_data/GM12878_combined_22_10kb_mmds_rep1.tsv").getCoords()
coords2 = dt.structure_from_file(
"hic_data/GM12878_combined_22_10kb_mmds_rep2.tsv").getCoords()
#rs[1] = rep_correlation(coords1, coords2)
rs[0] = rep_correlation(coords1, coords2)
#miniMDS
coords1 = dt.structure_from_file(
"hic_data/GM12878_combined_22_10kb_minimds_rep1.tsv").getCoords()
coords2 = dt.structure_from_file(
"hic_data/GM12878_combined_22_10kb_minimds_rep2.tsv").getCoords()
#rs[2] = rep_correlation(coords1, coords2)
rs[1] = rep_correlation(coords1, coords2)
#MOGEN
coords1 = np.loadtxt(
chromatinDiameter = 30 #diameter of heterochromatin (nm)
totDist = 0
count = 0
n = len(coords)
for i in range(1, n):
totDist += la.calcDistance(coords[i - 1], coords[i])
count += 1
avgDist = totDist / count #average distance between neighboring loci
physicalDist = kl * (res / bpPerKL)**(
1. / 2) #physical distance between neighboring loci (nm)
conversionFactor = avgDist / physicalDist
return chromatinDiameter / 2 * conversionFactor
mmds_structure = dt.structure_from_file(
"hic_data/GM12878_combined_22_10kb_mmds_coords.tsv")
cmds_structure = dt.structure_from_file(
"hic_data/GM12878_combined_22_10kb_cmds_coords.tsv")
minimds_structure = dt.structure_from_file(
"hic_data/GM12878_combined_22_10kb_minimds_coords.tsv")
mmds_res = mmds_structure.chrom.res
cmds_res = cmds_structure.chrom.res
minimds_res = minimds_structure.chrom.res
assert mmds_res == cmds_res == minimds_res
res = mmds_res
plot.plot_structure_interactive(mmds_structure, out_path="Fig9A.png")
plot.plot_structure_interactive(cmds_structure, out_path="Fig9B.png")
import sys
sys.path.append("..")
import data_tools as dt
import plotting as plot
struct1 = dt.structure_from_file("GM12878_combined_21_100kb_structure.tsv")
struct2 = dt.structure_from_file("K562_21_100kb_structure.tsv")
plot.plot_structures_interactive((struct1, struct2))
from scipy import stats as st
import misc
chroms = (1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
20, 21, 22, "X")
n = len(chroms)
mmds_rs = np.zeros(n)
cmds_rs = np.zeros(n)
minimds_rs = np.zeros(n)
mogen_rs = np.zeros(n)
for i, chrom in enumerate(chroms):
bedpath = "hic_data/GM12878_combined_{}_10kb.bed".format(chrom)
mmds_structure = dt.structure_from_file(
"hic_data/GM12878_combined_{}_10kb_mmds_coords.tsv".format(chrom))
contactMat = dt.matFromBed(bedpath, mmds_structure)
mmds_true_mat = at.contactToDist(contactMat)
at.makeSymmetric(mmds_true_mat)
for j in range(len(mmds_true_mat)): #remove diagonal
mmds_true_mat[j, j] = 0
mmds_distMat = misc.distMat(mmds_structure)
mmds_rs[i] = misc.pearson(mmds_true_mat, mmds_distMat)
cmds_structure = dt.structure_from_file(
"hic_data/GM12878_combined_{}_10kb_cmds_coords.tsv".format(chrom))
contactMat = dt.matFromBed(bedpath, cmds_structure)
cmds_true_mat = at.contactToDist(contactMat)
at.makeSymmetric(cmds_true_mat)
for j in range(len(cmds_true_mat)): #remove diagonal
cmds_true_mat[j, j] = 0
import linear_algebra as la
from matplotlib import pyplot as plt
import numpy as np
gene_name = sys.argv[1]
chrom_num = sys.argv[2]
gene_loc = int(sys.argv[3])
strain = sys.argv[4]
prefix = sys.argv[5]
res_kb = 32
chrom_name = "{}_{}".format(strain, chrom_num)
all_dists = []
for iteration in range(1, 11):
struct1 = dt.structure_from_file("{}_{}ctrl_{}_{}kb_structure.tsv".format(
iteration, prefix, chrom_name, res_kb))
struct2 = dt.structure_from_file(
"{}_{}galactose_{}_{}kb_structure.tsv".format(iteration, prefix,
chrom_name, res_kb))
#dt.make_compatible((struct1, struct2))
#struct1.rescale()
#struct2.rescale()
#r, t = la.getTransformation(struct1, struct2)
#struct1.transform(r,t)
all_dists.append([
la.calcDistance(coord1, coord2)
for coord1, coord2 in zip(struct1.getCoords(), struct2.getCoords())
])
chrom = 21
res_kb = 100
prefix1 = "GM12878_combined"
prefix2 = "K562"
path1 = "hic_data/{}_{}_{}kb.bed".format(prefix1, chrom, res_kb)
path2 = "hic_data/{}_{}_{}kb.bed".format(prefix2, chrom, res_kb)
ps = np.arange(0, 0.6, 0.1)
errors = np.zeros_like(ps)
for i, p in enumerate(ps):
os.system("python ../multimds.py -P {} {} {}".format(p, path1, path2))
structure1 = dt.structure_from_file("{}_{}_{}kb_structure.tsv".format(
prefix1, chrom, res_kb))
structure2 = dt.structure_from_file("{}_{}_{}kb_structure.tsv".format(
prefix2, chrom, res_kb))
dists1 = dt.normalized_dist_mat(path1, structure1)
dists2 = dt.normalized_dist_mat(path2, structure2)
errors[i] = np.mean(
(error(dists1,
structure1.getCoords()), error(dists1, structure1.getCoords())))
xs = ps
x_int_size = 0.1
ys = errors
y_int_size = 0.05
x_start = min(xs) - x_int_size / 4.
for i, comparison in enumerate(comparisons):
print comparison
with open("{}_design.txt".format(comparison)) as infile:
for line in infile:
prefix1, prefix2 = line.strip().split()
for chrom in range(1, 23):
path1 = "hic_data/{}_{}_100kb.bed".format(prefix1, chrom)
path2 = "hic_data/{}_{}_100kb.bed".format(prefix2, chrom)
if os.path.isfile(path1) and os.path.isfile(path2):
os.system("python ../multimds.py {} {}".format(
path1, path2))
#load structures
structure1 = dt.structure_from_file(
"{}_{}_100kb_structure.tsv".format(prefix1, chrom))
structure2 = dt.structure_from_file(
"{}_{}_100kb_structure.tsv".format(prefix2, chrom))
dists = [
la.calcDistance(coord1, coord2)
for coord1, coord2 in zip(structure1.getCoords(),
structure2.getCoords())
]
boxes[i].append(np.mean(dists))
infile.close()
#start with a frameless plot (extra room on the left)
plt.subplot2grid((10, 10), (0, 0), 9, 10, frameon=False)
import sys
sys.path.append("..")
import data_tools as dt
res_kb = int(sys.argv[1])
with open("chrom_sizes_{}kb.txt".format(res_kb), "w") as out:
for chrom in [
1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
20, 21, 22, "X"
]:
structure = dt.structure_from_file(
"hic_data/GM12878_combined_chr{}_{}kb_structure.tsv".format(
chrom, res_kb))
out.write(str(len(structure.getPoints())) + "\n")
out.close()
import sys
sys.path.append("../..")
import data_tools as dt
from matplotlib import pyplot as plt
import linear_algebra as la
struct1 = dt.structure_from_file("sim1_chr21_100kb_structure.tsv")
struct2 = dt.structure_from_file("sim2_chr21_100kb_structure.tsv")
#dt.make_compatible((struct1, struct2))
#struct1.rescale()
#struct2.rescale()
#r, t = la.getTransformation(struct1, struct2)
#struct1.transform(r,t)
gen_coords = struct1.getGenCoords()
dists = [
la.calcDistance(coord1, coord2)
for coord1, coord2 in zip(struct1.getCoords(), struct2.getCoords())
]
plt.subplot2grid((10, 10), (0, 0), 9, 10, frameon=False)
plt.plot(gen_coords, dists, lw=2)
#define offsets
xmin = min(gen_coords)
xmax = max(gen_coords)
x_range = xmax - xmin
x_start = xmin - x_range / 25.
x_end = xmax + x_range / 25.
import sys
sys.path.append("..")
import plotting as plot
import data_tools as dt
chroms = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, "X"]
structures = [dt.structure_from_file("hic_data/GM12878_combined_chr{}_10kb_structure.tsv".format(chrom)) for chrom in chroms]
plot.plot_structures_interactive(structures, out_path="Fig10.png")
x_means = []
y_means = []
z_means = []
x_lengths = []
y_lengths = []
z_lengths = []
for chrom in chroms:
path1 = "hic_data/{}_{}_{}kb.bed".format(cell_type1, chrom, res_kb)
path2 = "hic_data/{}_{}_{}kb.bed".format(cell_type2, chrom, res_kb)
if os.path.isfile(path1) and os.path.isfile(path2):
os.system("python ~/git/multimds/multimds.py --full {} {}".format(
path1, path2))
structure1 = dt.structure_from_file(
"hic_data/{}_{}_{}kb_structure.tsv".format(cell_type1, chrom,
res_kb))
structure2 = dt.structure_from_file(
"hic_data/{}_{}_{}kb_structure.tsv".format(cell_type2, chrom,
res_kb))
#plot.plot_structures_interactive((structure1, structure2))
#compartments
contacts1 = dt.matFromBed(path1, structure1)
contacts2 = dt.matFromBed(path2, structure2)
at.makeSymmetric(contacts1)
at.makeSymmetric(contacts2)
compartments1 = np.array(ca.get_compartments(contacts1))
import sys
sys.path.append("..")
import data_tools as dt
import linear_algebra as la
from matplotlib import pyplot as plt
import numpy as np
import compartment_analysis as ca
from scipy import stats as st
cell_type1 = sys.argv[1]
cell_type2 = sys.argv[2]
res_kb = int(sys.argv[3])
struct1 = dt.structure_from_file("{}_21_{}kb_structure.tsv".format(
cell_type1, res_kb))
struct2 = dt.structure_from_file("{}_21_{}kb_structure.tsv".format(
cell_type2, res_kb))
gen_coords = np.array(struct1.getGenCoords())
dists = np.array([
la.calcDistance(coord1, coord2)
for coord1, coord2 in zip(struct1.getCoords(), struct2.getCoords())
])
mat1 = dt.matFromBed("hic_data/{}_21_{}kb.bed".format(cell_type1, res_kb),
struct1)
comps1 = ca.get_compartments(mat1, struct1)
mat2 = dt.matFromBed("hic_data/{}_21_{}kb.bed".format(cell_type2, res_kb),
struct2)
comps2 = ca.get_compartments(mat2, struct2)
r, p = st.pearsonr(comps1, comps2)
import sys
sys.path.append("..")
import plotting as plot
import data_tools as dt
chroms = [
1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,
22, "X"
]
structures = [
dt.structure_from_file(
"hic_data/GM12878_combined_{}_10kb_structure.tsv".format(chrom))
for chrom in chroms
]
plot.plot_structures_interactive(structures, out_path="Fig10.png")
import sys
sys.path.append("..")
import data_tools as dt
import numpy as np
from mayavi import mlab
gene_name = sys.argv[1]
chrom_num = sys.argv[2]
gene_loc = int(sys.argv[3])
strain = sys.argv[4]
res_kb = 32
chrom_name = "{}_{}".format(strain, chrom_num)
struct1 = dt.structure_from_file("ctrl_{}_{}kb_structure.tsv".format(
chrom_name, res_kb))
struct2 = dt.structure_from_file("galactose_{}_{}kb_structure.tsv".format(
chrom_name, res_kb))
coords1 = np.array(struct1.getCoords())
coords2 = np.array(struct2.getCoords())
colors = np.zeros_like(struct1.getPoints(), dtype=int)
colors[struct1.get_rel_index(gene_loc)] = 1
mlab.figure(bgcolor=(1, 1, 1))
line = mlab.plot3d(coords1[:, 0], coords1[:, 1], coords1[:, 2], colors)
lut = line.module_manager.scalar_lut_manager.lut.table.to_array()
lut[0] = (0, 0, 255, 128)
lut[1:len(lut)] = (255, 0, 0, 128)
line.module_manager.scalar_lut_manager.lut.table = lut
line = mlab.plot3d(coords2[:, 0], coords2[:, 1], coords2[:, 2], colors)