Skip to content

Commit 1189668

Browse files
author
Alexander Lenail
committed
2 parents 37be858 + c12f978 commit 1189668

File tree

2 files changed

+245
-0
lines changed

2 files changed

+245
-0
lines changed

‎interactomes/PCNet.05_2018.oi2

+3
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,3 @@
1+
version https://git-lfs.github.com/spec/v1
2+
oid sha256:18bba1b9612ffde9b729deac04216a666da50c8ac4571e7726cd6bb9ca406d41
3+
size 44161527

‎interactomes/PreProcess_PCNet_For_OmicsIntegrator.ipynb

+242
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,242 @@
1+
{
2+
"cells": [
3+
{
4+
"cell_type": "markdown",
5+
"metadata": {},
6+
"source": [
7+
"# PreProcessing PCNet for OmicsIntegrator\n",
8+
"\n",
9+
"All Fraenkel-lab interactomes have been pre-processed to have 3 columns: 2 interactors and a scalar confidence\n",
10+
"However, OmicsIntegrator requires that edges have a cost, not a confidence. This notebook sets costs on the edges and augments those interactomes for use in OmicsIntegrator."
11+
]
12+
},
13+
{
14+
"cell_type": "code",
15+
"execution_count": 1,
16+
"metadata": {},
17+
"outputs": [],
18+
"source": [
19+
"import numpy as np\n",
20+
"import pandas as pd\n",
21+
"import matplotlib.pyplot as plt\n",
22+
"%matplotlib inline"
23+
]
24+
},
25+
{
26+
"cell_type": "code",
27+
"execution_count": 2,
28+
"metadata": {},
29+
"outputs": [
30+
{
31+
"data": {
32+
"text/html": [
33+
"<div>\n",
34+
"<style scoped>\n",
35+
" .dataframe tbody tr th:only-of-type {\n",
36+
" vertical-align: middle;\n",
37+
" }\n",
38+
"\n",
39+
" .dataframe tbody tr th {\n",
40+
" vertical-align: top;\n",
41+
" }\n",
42+
"\n",
43+
" .dataframe thead th {\n",
44+
" text-align: right;\n",
45+
" }\n",
46+
"</style>\n",
47+
"<table border=\"1\" class=\"dataframe\">\n",
48+
" <thead>\n",
49+
" <tr style=\"text-align: right;\">\n",
50+
" <th></th>\n",
51+
" <th>protein1</th>\n",
52+
" <th>protein2</th>\n",
53+
" <th>confidence</th>\n",
54+
" </tr>\n",
55+
" </thead>\n",
56+
" <tbody>\n",
57+
" <tr>\n",
58+
" <th>0</th>\n",
59+
" <td>A1BG</td>\n",
60+
" <td>A2M</td>\n",
61+
" <td>NaN</td>\n",
62+
" </tr>\n",
63+
" <tr>\n",
64+
" <th>1</th>\n",
65+
" <td>A1BG</td>\n",
66+
" <td>ABCC6</td>\n",
67+
" <td>NaN</td>\n",
68+
" </tr>\n",
69+
" <tr>\n",
70+
" <th>2</th>\n",
71+
" <td>A1BG</td>\n",
72+
" <td>ACOT12</td>\n",
73+
" <td>NaN</td>\n",
74+
" </tr>\n",
75+
" <tr>\n",
76+
" <th>3</th>\n",
77+
" <td>A1BG</td>\n",
78+
" <td>ADH1A</td>\n",
79+
" <td>NaN</td>\n",
80+
" </tr>\n",
81+
" <tr>\n",
82+
" <th>4</th>\n",
83+
" <td>A1BG</td>\n",
84+
" <td>ADH4</td>\n",
85+
" <td>NaN</td>\n",
86+
" </tr>\n",
87+
" </tbody>\n",
88+
"</table>\n",
89+
"</div>"
90+
],
91+
"text/plain": [
92+
" protein1 protein2 confidence\n",
93+
"0 A1BG A2M NaN\n",
94+
"1 A1BG ABCC6 NaN\n",
95+
"2 A1BG ACOT12 NaN\n",
96+
"3 A1BG ADH1A NaN\n",
97+
"4 A1BG ADH4 NaN"
98+
]
99+
},
100+
"execution_count": 2,
101+
"metadata": {},
102+
"output_type": "execute_result"
103+
}
104+
],
105+
"source": [
106+
"pcnet = pd.read_pickle(\"../../interactomes/PCNet/PCNet.05_2018.cleaned.namespace-mapped.full.pickle\")\n",
107+
"pcnet.head()"
108+
]
109+
},
110+
{
111+
"cell_type": "markdown",
112+
"metadata": {},
113+
"source": [
114+
"### PCNet is relatively unique in that we don't have confidences for the edges. We'll need to set them arbitrarily"
115+
]
116+
},
117+
{
118+
"cell_type": "code",
119+
"execution_count": 3,
120+
"metadata": {},
121+
"outputs": [
122+
{
123+
"data": {
124+
"text/html": [
125+
"<div>\n",
126+
"<style scoped>\n",
127+
" .dataframe tbody tr th:only-of-type {\n",
128+
" vertical-align: middle;\n",
129+
" }\n",
130+
"\n",
131+
" .dataframe tbody tr th {\n",
132+
" vertical-align: top;\n",
133+
" }\n",
134+
"\n",
135+
" .dataframe thead th {\n",
136+
" text-align: right;\n",
137+
" }\n",
138+
"</style>\n",
139+
"<table border=\"1\" class=\"dataframe\">\n",
140+
" <thead>\n",
141+
" <tr style=\"text-align: right;\">\n",
142+
" <th></th>\n",
143+
" <th>protein1</th>\n",
144+
" <th>protein2</th>\n",
145+
" <th>cost</th>\n",
146+
" </tr>\n",
147+
" </thead>\n",
148+
" <tbody>\n",
149+
" <tr>\n",
150+
" <th>0</th>\n",
151+
" <td>A1BG</td>\n",
152+
" <td>A2M</td>\n",
153+
" <td>1.0</td>\n",
154+
" </tr>\n",
155+
" <tr>\n",
156+
" <th>1</th>\n",
157+
" <td>A1BG</td>\n",
158+
" <td>ABCC6</td>\n",
159+
" <td>1.0</td>\n",
160+
" </tr>\n",
161+
" <tr>\n",
162+
" <th>2</th>\n",
163+
" <td>A1BG</td>\n",
164+
" <td>ACOT12</td>\n",
165+
" <td>1.0</td>\n",
166+
" </tr>\n",
167+
" <tr>\n",
168+
" <th>3</th>\n",
169+
" <td>A1BG</td>\n",
170+
" <td>ADH1A</td>\n",
171+
" <td>1.0</td>\n",
172+
" </tr>\n",
173+
" <tr>\n",
174+
" <th>4</th>\n",
175+
" <td>A1BG</td>\n",
176+
" <td>ADH4</td>\n",
177+
" <td>1.0</td>\n",
178+
" </tr>\n",
179+
" </tbody>\n",
180+
"</table>\n",
181+
"</div>"
182+
],
183+
"text/plain": [
184+
" protein1 protein2 cost\n",
185+
"0 A1BG A2M 1.0\n",
186+
"1 A1BG ABCC6 1.0\n",
187+
"2 A1BG ACOT12 1.0\n",
188+
"3 A1BG ADH1A 1.0\n",
189+
"4 A1BG ADH4 1.0"
190+
]
191+
},
192+
"execution_count": 3,
193+
"metadata": {},
194+
"output_type": "execute_result"
195+
}
196+
],
197+
"source": [
198+
"pcnet['cost'] = 1.0\n",
199+
"del pcnet['confidence']\n",
200+
"\n",
201+
"pcnet.head()"
202+
]
203+
},
204+
{
205+
"cell_type": "code",
206+
"execution_count": 4,
207+
"metadata": {},
208+
"outputs": [],
209+
"source": [
210+
"pcnet.to_csv('PCNet.05_2018.oi2', sep='\\t', index=False)\n"
211+
]
212+
},
213+
{
214+
"cell_type": "code",
215+
"execution_count": null,
216+
"metadata": {},
217+
"outputs": [],
218+
"source": []
219+
}
220+
],
221+
"metadata": {
222+
"kernelspec": {
223+
"display_name": "Python 3",
224+
"language": "python",
225+
"name": "python3"
226+
},
227+
"language_info": {
228+
"codemirror_mode": {
229+
"name": "ipython",
230+
"version": 3
231+
},
232+
"file_extension": ".py",
233+
"mimetype": "text/x-python",
234+
"name": "python",
235+
"nbconvert_exporter": "python",
236+
"pygments_lexer": "ipython3",
237+
"version": "3.6.5"
238+
}
239+
},
240+
"nbformat": 4,
241+
"nbformat_minor": 2
242+
}

0 commit comments

Comments
 (0)