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
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
|
#!/home/jziebart/python/Python-2.7.15/python
import os
import sys
import math
#sys.path.append('/home/jziebart/.local/bin')
#sys.path.append('/home/jziebart/.local/lib')
import plotly
import plotly.graph_objs as go
import csv
import string
def mean_stdev(y):
mean = sum(y)
mean = sum(y)/len(y)
stdev = 0
for yi in y:
stdev = stdev + (yi - mean)**2
stdev = stdev/(len(y)-1)
stdev = math.sqrt(stdev)
return mean,stdev;
def standardize(y):
mean,stdev = mean_stdev(y)
ystd = []
for yi in y:
yi = (yi - mean)/stdev
ystd.append(yi)
return ystd
netID = sys.argv[-1]
outfile = netID+"violin_plotly.html"
filename=netID+"continuous_input.txt"
f=open(filename,"r")
#Read the first line to get the variable names
line=f.readline()
line = map(string.strip,line.strip().split("\t"))
varNames = line
line=f.readline()
line = map(string.strip,line.strip().split("\t"))
for i in range(len(line)):
line[i] = int(line[i])
cd_types = line
cNames = []
for i in range(len(varNames)):
if cd_types[i] == 1:
cNames.append(varNames[i])
#Read in original data
data = []
line = f.readline()
while line:
line = map(string.strip,line.strip().split("\t"))
temp = []
for i in range(len(varNames)):
if cd_types[i] == 1:
temp.append(float(line[i]))
data.append(temp)
line = f.readline()
#Read in data for violin plots
filename2=netID+"violin_orig.txt"
f2=open(filename2,"r")
line = f2.readline()
pdf_data = []
while line:
line = line.strip()
if line == "Data for new node":
line = f2.readline()
pdf_data.append([line.strip()])
else:
pdf_data[-1].append(float(line.strip()))
line = f2.readline()
pdf_data2 = []
for i in range(len(cNames)):
for j in range(len(pdf_data)):
if cNames[i] == pdf_data[j][0]:
pdf_data2.append(pdf_data[j][1:])
del pdf_data
layout = go.Layout(
title="<br>Original distributions",
titlefont=dict(
family='Arial, sans-serif',
size=24,
color='black'
),
yaxis=dict(title="Distributions of standardized data"),
legend=dict(orientation='h'),
margin=dict(t=10,l=70,b=40)
)
fig = go.Figure(layout=layout)
for i in range(len(cNames)):
y = []
for j in range(len(data)):
y.append(data[j][i])
y_stand = standardize(y)
#Add traces to violin plot
if i == 1:
fig.add_trace(go.Violin(y=y_stand,x0=cNames[i],side='negative',legendgroup='Data',name='Fit to data',fillcolor='blue',line=dict(color='blue'),hoverinfo='none',points='all',scalegroup=cNames[i]))
fig.add_trace(go.Violin(y=pdf_data2[i],x0=cNames[i],side='positive',legendgroup='Network parameters',name='Network parameters',fillcolor='orange',line=dict(color='orange'),hoverinfo='none',points=False,scalegroup=cNames[i]))
else:
fig.add_trace(go.Violin(y=y_stand,x0=cNames[i],side='negative',legendgroup='Data',name='Data',fillcolor='blue',line=dict(color='blue'),showlegend=False,hoverinfo='none',points='all',scalegroup=cNames[i]))
fig.add_trace(go.Violin(y=pdf_data2[i],x0=cNames[i],side='positive',legendgroup='Network parameters',name='Network parameters',fillcolor='orange',line=dict(color='orange'),showlegend=False,hoverinfo='none',points=False,scalegroup=cNames[i]))
plotly.offline.plot(fig,filename=outfile)
|
