-
Notifications
You must be signed in to change notification settings - Fork 0
/
test.py
70 lines (58 loc) · 2.22 KB
/
test.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
from data_reader import DataReader
from co_graph import CoGraph
import numpy as np
import cluster_merge as cm
from log import output
import matplotlib.pyplot as plt
import scipy
from scipy.linalg import logm, expm
rd = DataReader()
rd.pre_process_cell(threshold=1850, original=True)
rd.pre_process_gene(threshold=2600, original=False)
genes = rd.get_gene_data()
collect = dict()
for x in range(len(genes)):
for y in range(x + 1, len(genes)):
X = genes[x]
Y = genes[y]
# matrix dimension
N = 15
matrix = [[0 for _ in range(N)] for _ in range(N)]
for k in range(len(X)):
xcord = X[k]
ycord = Y[k]
if xcord >= N or ycord >= N: continue
matrix[int(xcord)][int(ycord)] += 1
# for i in range(len(matrix[0])):
# matrix[0][i] = matrix[0][i] if matrix[0][i] != 0 else 1
# from math import log
# matrix = [[log(item if item != 0 else 1, 10) for item in row] for row in matrix]
for k in range(len(matrix) - 1, -1, -1):
result = ''
for j in range(len(matrix[k])):
result += '{:4}'.format(matrix[k][j])
for k in range(1, N - 5):
# for i in range(len(matrix[k])):
# matrix[k][i] = matrix[k][i] if matrix[k][i] != 0 else 1
# print matrix[k]
# print matrix[0]
chi = False
merge = [[0 for _ in range(N)] for _ in range(2)]
for index in range(N):
for i in range(k):
merge[0][index] += matrix[i][index]
merge[0][index] = merge[0][index] / ((k + 1) * 1.0)
if merge[0][index] == 0.0:
chi = True
for index in range(N):
for i in range(N - k):
merge[1][index] += matrix[i][index]
merge[1][index] = merge[1][index] / ((20 - k) * 1.0)
if merge[1][index] == 0.0:
chi = True
if chi:
continue
chisq, p_value = scipy.stats.chisquare(merge[0], f_exp=merge[1])
if p_value >= 0.05:
collect.update({k: collect[k] + 1 if k in collect else 1})
print collect