Repositorio del Broad Institute: https://gdac.broadinstitute.org Datos de cancer a nivel mundial (Acceso 4)
In [14]:
import numpy as np #libreria de datos numericos
%matplotlib inline
import seaborn as sns
sns.set()
# inline permite imprimir en jupyter
# 1. generar numeros aleatorios
# 2. vector
# 3. graficar la distribución (poisson, beta, normal)
n = np.random.beta(5, 1, 1000) #genera 100 valores aleatorios con los parametros a =5 y b = 1
x = np.random.beta (0.5, 0.5 , 1000)
sns.distplot(n)
sns.distplot(x)
Out[14]:
<matplotlib.axes._subplots.AxesSubplot at 0x10fcd39d0>
In [6]:
import pandas as pd
DF = pd.read_csv('/Users/camilogarcia/Downloads/gdac.broadinstitute.org_BRCA.Merge_rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__gene_expression__data.Level_3.2016012800.0.0/BRCA.rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__gene_expression__data.data.txt', sep='\t')
/Users/camilogarcia/anaconda/lib/python2.7/site-packages/IPython/core/interactiveshell.py:2717: DtypeWarning: Columns (1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,516,517,518,519,520,521,522,523,524,525,526,527,528,529,530,531,532,533,534,535,536,537,538,539,540,541,542,543,544,545,546,547,548,549,550,551,552,553,554,555,556,557,558,559,560,561,562,563,564,565,566,567,568,569,570,571,572,573,574,575,576,577,578,579,580,581,582,583,584,585,586,587,588,589,590,591,592,593,594,595,596,597,598,599,600,601,602,603,604,605,606,607,608,609,610,611,612,613,614,615,616,617,618,619,620,621,622,623,624,625,626,627,628,629,630,631,632,633,634,635,636,637,638,639,640,641,642,643,644,645,646,647,648,649,650,651,652,653,654,655,656,657,658,659,660,661,662,663,664,665,666,667,668,669,670,671,672,673,674,675,676,677,678,679,680,681,682,683,684,685,686,687,688,689,690,691,692,693,694,695,696,697,698,699,700,701,702,703,704,705,706,707,708,709,710,711,712,713,714,715,716,717,718,719,720,721,722,723,724,725,726,727,728,729,730,731,732,733,734,735,736,737,738,739,740,741,742,743,744,745,746,747,748,749,750,751,752,753,754,755,756,757,758,759,760,761,762,763,764,765,766,767,768,769,770,771,772,773,774,775,776,777,778,779,780,781,782,783,784,785,786,787,788,789,790,791,792,793,794,795,796,797,798,799,800,801,802,803,804,805,806,807,808,809,810,811,812,813,814,815,816,817,818,819,820,821,822,823,824,825,826,827,828,829,830,831,832,833,834,835,836,837,838,839,840,841,842,843,844,845,846,847,848,849,850,851,852,853,854,855,856,857,858,859,860,861,862,863,864,865,866,867,868,869,870,871,872,873,874,875,876,877,878,879,880,881,882,883,884,885,886,887,888,889,890,891,892,893,894,895,896,897,898,899,900,901,902,903,904,905,906,907,908,909,910,911,912,913,914,915,916,917,918,919,920,921,922,923,924,925,926,927,928,929,930,931,932,933,934,935,936,937,938,939,940,941,942,943,944,945,946,947,948,949,950,951,952,953,954,955,956,957,958,959,960,961,962,963,964,965,966,967,968,969,970,971,972,973,974,975,976,977,978,979,980,981,982,983,984,985,986,987,988,989,990,991,992,993,994,995,996,997,998,999,1000,1001,1002,1003,1004,1005,1006,1007,1008,1009,1010,1011,1012,1013,1014,1015,1016,1017,1018,1019,1020,1021,1022,1023,1024,1025,1026,1027,1028,1029,1030,1031,1032,1033,1034,1035,1036,1037,1038,1039,1040,1041,1042,1043,1044,1045,1046,1047,1048,1049,1050,1051,1052,1053,1054,1055,1056,1057,1058,1059,1060,1061,1062,1063,1064,1065,1066,1067,1068,1069,1070,1071,1072,1073,1074,1075,1076,1077,1078,1079,1080,1081,1082,1083,1084,1085,1086,1087,1088,1089,1090,1091,1092,1093,1094,1095,1096,1097,1098,1099,1100,1101,1102,1103,1104,1105,1106,1107,1108,1109,1110,1111,1112,1113,1114,1115,1116,1117,1118,1119,1120,1121,1122,1123,1124,1125,1126,1127,1128,1129,1130,1131,1132,1133,1134,1135,1136,1137,1138,1139,1140,1141,1142,1143,1144,1145,1146,1147,1148,1149,1150,1151,1152,1153,1154,1155,1156,1157,1158,1159,1160,1161,1162,1163,1164,1165,1166,1167,1168,1169,1170,1171,1172,1173,1174,1175,1176,1177,1178,1179,1180,1181,1182,1183,1184,1185,1186,1187,1188,1189,1190,1191,1192,1193,1194,1195,1196,1197,1198,1199,1200,1201,1202,1203,1204,1205,1206,1207,1208,1209,1210,1211,1212,1213,1214,1215,1216,1217,1218,1219,1220,1221,1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have mixed types. Specify dtype option on import or set low_memory=False.
interactivity=interactivity, compiler=compiler, result=result)
In [7]:
DF = DF.drop([0]) # eliminar la prmiera fila
In [8]:
DF.head(100)
Out[8]:
Hybridization REF
TCGA-A1-A0SB-01A-11R-A144-07
TCGA-A1-A0SB-01A-11R-A144-07.1
TCGA-A1-A0SB-01A-11R-A144-07.2
TCGA-A1-A0SD-01A-11R-A115-07
TCGA-A1-A0SD-01A-11R-A115-07.1
TCGA-A1-A0SD-01A-11R-A115-07.2
TCGA-A1-A0SE-01A-11R-A084-07
TCGA-A1-A0SE-01A-11R-A084-07.1
TCGA-A1-A0SE-01A-11R-A084-07.2
...
TCGA-GM-A2DD-01A-11R-A180-07.2
TCGA-GM-A2DF-01A-11R-A180-07
TCGA-GM-A2DF-01A-11R-A180-07.1
TCGA-GM-A2DF-01A-11R-A180-07.2
TCGA-GM-A2DH-01A-11R-A180-07
TCGA-GM-A2DH-01A-11R-A180-07.1
TCGA-GM-A2DH-01A-11R-A180-07.2
TCGA-GM-A2DK-01A-21R-A180-07
TCGA-GM-A2DK-01A-21R-A180-07.1
TCGA-GM-A2DK-01A-21R-A180-07.2
1
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0.648804765767191
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3.31043046357616
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2.25846925972396
0.297493981144456
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0.12295093161439
47
1.46486825595985
0.314193796680778
76
2.37892095357591
0.445333755567924
27
0.846925972396487
0.192784015000064
4
?|10357
269
21.1477987421384
5.29354054052308
175
13.7578616352201
2.68707552797622
392
30.8176100628931
4.05941035836283
...
3.93345184457586
266
20.9119496855346
4.45669164217304
467
36.7138364779874
6.85835726947309
232
18.2201257861635
4.15170457833354
5
?|10431
1921
85.8550983899821
21.5048610324708
3676
164.30053667263
32.1094332306395
5835
260.711091234347
34.3742365295763
...
42.5666139352044
4197
187.663685152057
40.0023247303838
5796
259.050983899821
48.4224671517638
3282
146.748658318426
33.4112209880393
6
?|136542
0
0
0
0
0
0
0
0
0
...
0
0
0
0
0
0
0
0
0
0
7
?|155060
1007
17.2432804962095
4.34293312170185
453
7.73121984838043
1.5244027886466
655
11.1664369400414
1.48654443723434
...
2.12533597461052
811
13.9093728463129
2.97790961155424
841
14.3518263266713
2.70681720121152
713
12.1929703652653
2.79632532220311
8
?|26823
9
0.827205882352941
0.20705927491495
18
1.64338235294118
0.323126477355796
13
1.18382352941176
0.157390478892857
...
0.169536146188008
9
0.827205882352941
0.176291622621341
12
1.10294117647059
0.20603579906403
4
0.367647058823529
0.0836867428949078
9
?|280660
0
0
0
0
0
0
0
0
0
...
0
0
0
0
0
0
0
0
0
0
10
?|317712
0
0
0
0
0
0
0
0
0
...
0
0
0
0
0
0
0
0
0
0
11
?|340602
5
0.128932439401753
0.0322732925201229
4
0.103145951521403
0.0201456425054786
1
0.0072202166064982
0.00339669220921625
...
0.130802514026436
0
0
0
0
0
0
2
0.0515729757607014
0.0117394502668463
12
?|388795
8
0.0911386013632921
0.0252776224979624
6
0.0757384498863923
0.0147926284340279
8
0.100984599848523
0.0133020675459133
...
0.0349259013606197
9
0.113607674829588
0.0242117249952056
26
0.32441302701338
0.0613096512236312
21
0.263064882605403
0.0603406558212211
13
?|390284
1
0.151057401812689
0.0378114285175337
2
0.302114803625378
0.059006647761515
12
1.81268882175227
0.238774121824905
...
0.243804246481848
1
0.151057401812689
0.0321928978536453
8
1.202416918429
0.225747179639138
6
0.906344410876133
0.206309311789259
14
?|391343
0
0
0
2
0.0380807311500381
0.00743762391814983
2
0.0380807311500381
0.00501613571490503
...
0.0526814528901045
2
0.0380807311500381
0.00811565056325712
8
0.152322924600152
0.0284548044404245
0
0
0
15
?|391714
4
0.141435678749112
0.0355809035943245
2
0.0504619758351102
0.0138814501841233
2
0.0710732054015636
0.00936202728311345
...
0.0327745783675467
0
0
0
2
0.0632551528073916
0.0132768863647041
0
0
0
16
?|404770
0
0
0
0
0
0
0
0
0
...
0
0
0
0
0
0
0
0
0
0
17
?|441362
0
0
0
2
0.0618429189857761
0.0120786644459255
2
0.04143475572047
0.0081461795840078
...
0
0
0
0
6
0.185528756957328
0.0346578462247471
0
0
0
18
?|442388
0
0
0
0
0
0
0
0
0
...
0.118605534370211
0
0
0
0
0
0
0
0
0
19
?|553137
0
0
0
8
0.162866449511401
0.0318097726531946
8
0.162866449511401
0.0214533752236818
...
0.168983911184138
256
5.16734527687296
1.11070740738049
28
0.570032573289902
0.106485385835481
6
0.115228013029316
0.0278047158803928
20
?|57714
1408
14.6589390142022
3.68043872968662
4816
50.1988304093567
9.82270897765664
3613
37.6083959899749
4.96990198783016
...
4.60367827543443
847
8.81516290726817
1.88502595312332
10867
113.260651629073
21.1990239394541
743
7.73767752715121
1.76616081788735
21
?|645851
101
5.75635103926097
1.45966959211278
110
6.22863741339492
1.24043420611822
98
5.62586605080831
0.745318991893407
...
0.545804590729984
76
4.36951501154734
0.935155356127369
292
16.6662817551963
3.14938169839521
38
2.19399538106236
0.499414650439819
22
?|652919
142
2.13533834586466
0.534500079152216
160
2.40601503759398
0.469923618864637
154
2.31578947368421
0.30504441318052
...
0.124819394246088
33
0.496240601503759
0.105757300227178
204
3.06766917293233
0.573058366840345
21
0.315789473684211
0.0718825075813103
23
?|653553
81
10.6299212598425
2.66079320205668
749
98.2808398950131
19.1979909532638
1871
245.115485564304
32.3431873185227
...
92.8025735023259
720
94.3333333333333
20.1370378385322
467
61.249343832021
11.448596386837
5429
711.650918635171
162.177439622042
24
?|728045
0
0
0
0
0
0
0
0
0
...
0
0
0
0
0
0
0
0
0
0
25
?|728603
0
0
0
2
0.053475935828877
0.0104444921973591
3
0.0802139037433155
0.0105660741074925
...
0
0
0
0
2
0.053475935828877
0.00998961450007417
0
0
0
26
?|728788
38
2.3393085787452
0.608952814204275
9
0.57618437900128
0.112535725788446
9
0.567221510883483
0.0758971520397347
...
0.103328048124829
8
0.512163892445583
0.109150823964728
19
1.14852752880922
0.227228555177743
6
0.345710627400768
0.0874371090937833
27
?|729884
0
0
0
48
1.12359550561798
0.219451689989455
22
0.51498127340824
0.0678352510584021
...
1.65694596808092
8
0.187265917602996
0.0399095475264292
2
0.0468164794007491
0.00874558947337954
8
0.187265917602996
0.042626955182425
28
?|8225
1642
56.5437629221227
14.1630510145669
1497
51.526533425224
10.0751919408563
5022
172.879393521709
22.7951943932545
...
11.774758558403
2875
99.0144727773949
21.1134158649037
4834
166.439007580979
31.1171328196349
2123
73.0840799448656
16.6524506564858
29
?|90288
22
0.500230520977409
0.126944593114191
77
1.74965421853389
0.346681058436545
682
15.6855693868142
2.0708985634316
...
0.191343700261984
6
0.138312586445367
0.0294767612435867
183
4.17750115260489
0.7880465601822
92
2.10235131396957
0.482751741402069
30
A1BG|1
164
3.19088766692852
0.806188368281932
546
10.6893165750196
2.09427247119944
1341
26.1417910447761
3.46900066210208
...
3.21039932443686
227
4.44776119402985
0.950069821692596
461
8.97721916732129
1.6912307486408
855
16.7062058130401
3.82211094415549
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
71
ABCA7|10347
408
10.4447300771208
2.62537676012128
583
14.987146529563
2.92716962428865
2140
54.8318766066838
7.246497920028
...
7.87728565722501
1279
32.8071979434447
7.00711111230997
2566
65.8174807197943
12.3224591283923
1519
39.0066838046273
8.88860776051498
72
ABCA8|10351
548
7.35831318828901
1.84220773460607
1060
14.2358313188289
2.78042874477641
704
9.45474080042976
1.24541366649044
...
1.74026144580202
298
4.00080580177276
0.852925881946782
277
3.7061509535321
0.694939620587352
1474
19.7810905183991
4.50609165395778
73
ABCA9|10350
322
2.6558784676354
0.665458664837479
649
5.34296565389696
1.04654467185278
1176
9.70805812417437
1.27895557525698
...
1.09840162348624
227
1.87301849405548
0.399418389370764
668
5.50511889035667
1.03026972002251
697
5.74900924702774
1.30991309981739
74
ABCB10|23456
1285
16.6006216006216
4.16537786804071
2419
31.2781662781663
6.11835972410252
3708
47.962185962186
6.32519513238267
...
2.86345277524278
1513
19.5405335405335
4.17567983004381
3457
44.6943796943797
8.36295804209201
1631
21.1015281015281
4.80783697538899
75
ABCB11|8647
4
0.0609013398294763
0.0152443152732079
14
0.213154689403167
0.041631669568645
11
0.153166869671133
0.0220609159958506
...
0.00702098534761543
6
0.0913520097442144
0.0194686647799451
20
0.292935444579781
0.0568836148451239
4
0.0609013398294763
0.0138628465696802
76
ABCB1|5243
78
1.69270833333333
0.423704627372259
892
19.3576388888889
3.78077924585131
1416
30.7269965277778
4.04776026485988
...
1.92140965679742
70
1.51909722222222
0.323745418085487
731
15.8637152777778
2.96343388306562
355
7.70399305555556
1.75364407420406
77
ABCB4|5244
41
0.526180698151951
0.131709162323267
201
2.57571868583162
0.503820749771734
137
1.72458932238193
0.231598436481733
...
0.55038325897996
56
0.711755646817248
0.15316415672874
177
2.26771047227926
0.424340670351585
88
1.12936344969199
0.257074676326041
78
ABCB5|340273
161
3.53404539385848
0.89675515671023
185
4.05117935024477
0.804021378655178
264
5.84023141967067
0.773810927961265
...
1.0569035762357
165
3.62483311081442
0.782472236883329
235
5.19759679572764
0.976843812206852
150
3.29906542056075
0.759772832690752
79
ABCB6|10058
2204
36.7721349816238
9.21628619372711
2993
49.988306047444
9.76560020453073
4492
74.9906448379552
9.884780615425
...
13.0422180379206
1207
20.1637153357835
4.29723019438517
3934
65.7113264283328
12.2768790910384
6316
105.475108586702
24.0176757984953
80
ABCB7|22
2125
46.1154513888889
11.5432350405904
2116
45.9201388888889
8.96875435450826
3533
76.6484375
10.099390547846
...
4.6233919866688
572
12.4131944444444
2.64546255921284
2861
62.0707465277778
11.5983369896727
622
13.4982638888889
3.07258201170401
81
ABCB8|11194
842
9.53517930095325
2.39176594432448
2662
30.1999546073536
5.90014247491167
4484
50.8429414434862
6.70278231784332
...
3.64745128675752
2828
32.0497049477985
6.83947832684205
1867
21.166817975488
3.95785760417203
1560
17.6861098502043
4.02972750172121
82
ABCB9|23457
702
11.0435606060606
2.77333937916388
1222
19.2168560606061
3.76690765465169
868
13.6404671717172
1.8045484899324
...
3.12592972573672
1406
22.1455176767677
4.72920579561761
993
15.6212121212121
2.92768545791236
993
15.6161616161616
3.56746441113368
83
ABCC10|89845
1582
15.7167859984089
3.93787829192092
1374
13.6426014319809
2.66864253799229
2719
27.0196897374702
3.56162296352219
...
3.38883469301503
1867
18.5535003977725
3.95673636374347
2379
23.6054097056484
4.41936134794302
1733
17.2299124900557
3.9228243952695
84
ABCC11|85320
74
1.14127082048118
0.285673389916246
5552
85.6156693399136
16.7238162663648
7102
109.512646514497
14.4278514335122
...
27.8396968594701
104
1.60394818013572
0.3418285983078
480
7.40098704503393
1.3828929634896
108
1.66563849475632
0.379145860468972
85
ABCC12|94160
3
0.0237154150197628
0.00781084845390284
135
1.38631162887456
0.274257546829966
17
0.168920324526732
0.0232921084444342
...
0.112718436283935
1
0.00208029956313709
0.00221673584138893
17
0.168504264614104
0.0330320204865153
0
0
0
86
ABCC13|150000
18
0.320315299175923
0.0807167649973005
21
0.376209243998567
0.0734781814027751
54
0.967395198853458
0.127428898050232
...
0.128048081750025
17
0.304550340379792
0.0649048499543039
30
0.53744177714081
0.100397236376596
19
0.34037979218918
0.0774799511431178
87
ABCC1|4363
5129
40.253728999843
10.078885913454
4951
38.8607316690218
7.59137802051054
9183
72.0309310723818
9.49614504890476
...
18.7670045423228
3420
26.8412623645784
5.72193503348777
8514
66.8158266603863
12.4859829318803
3807
29.8726644685194
6.80310543371398
88
ABCC2|1244
54
0.520490991882795
0.133803498974935
390
3.84814888140962
0.754025753270043
38
0.374975252425262
0.0495496090594876
...
2.3120823389457
102
0.999010097010493
0.215184442156954
298
2.91704612947931
0.551060441131591
25
0.247475747376757
0.0563323947421672
89
ABCC3|8714
118
2.77006610009443
0.697279874899825
2786
65.6808309726157
12.8455912038823
2814
66.3087818696884
8.75048533946565
...
11.0113646903716
669
15.7625118035883
3.36579938990244
1230
28.9338999055713
5.4242474767754
2636
62.1166194523135
14.1649492827445
90
ABCC4|10257
320
6.0882800608828
1.52396746901719
861
16.3812785388128
3.1994603409821
769
14.630898021309
1.92723637097887
...
2.53117208212811
598
11.3774733637747
2.42473280645162
684
13.0079908675799
2.43103426840846
261
4.96575342465753
1.1303442259504
91
ABCC5|10057
3084
45.1941348973607
11.3190784388306
14156
207.512609970674
40.5401280044977
2012
29.4844574780059
3.88604299755562
...
5.60871311547259
2122
31.091495601173
6.63100058071528
12866
188.563049853372
35.2411042368584
4917
72.0774193548387
16.4112402389266
92
ABCC6P1|653190
1
0.0179856115107914
0.00450200821557685
37
0.665467625899281
0.129973815671812
93
1.6726618705036
0.220329250363791
...
0.518365914603621
2
0.0359712230215827
0.00766607855363784
52
0.935251798561151
0.174710452155973
4
0.0719424460431655
0.0163761108398669
93
ABCC6P2|730013
0
0
0
36
2.54957507082153
0.497962616661624
152
10.7648725212465
1.41798909552109
...
10.5650315689626
21
1.48725212464589
0.316958686941485
170
12.0396600566572
2.24907822207761
20
1.39093484419263
0.322419179425141
94
ABCC6|368
43
1.05009920634921
0.266949435560544
267
6.62202380952381
1.29336074137386
741
18.328373015873
2.42081546106632
...
12.4948812503047
115
2.82242063492063
0.607848540078874
631
15.6116071428571
2.92347356687811
281
6.95039682539683
1.58639512225784
95
ABCC8|6833
0
0
0
1314
18.5125599774203
3.62178906823409
3521
49.493649449619
6.54528975103391
...
1.61391903432942
4
0.0564493367202935
0.012030312378839
1667
23.379621789444
4.39465500775278
25
0.352808354501835
0.0803090391878878
96
ABCC9|10060
2888
33.7519869097709
8.44904236557011
5518
64.4878447872838
12.5962089594672
5348
62.4927536231884
8.23350251607032
...
8.86597162813958
2762
32.275829827022
6.87972310929297
5224
61.0516596540439
11.4057205817537
3371
39.3957456755493
8.96837059388216
97
ABCD1|215
554
13.3014492753623
3.34958110771701
1138
27.4521739130435
5.36872127186279
1524
36.73961352657
4.84896027012249
...
18.0389735604836
6262
150.995169082126
32.2352307367166
2196
52.8806763285024
9.90882892194314
1159
27.8980676328502
6.37248268698887
98
ABCD2|225
22
0.205953941209511
0.0515526722457742
93
0.870623478749298
0.170043216442868
74
0.692754165886538
0.0912521584593902
...
0.304346109277405
89
0.833177307620296
0.177564234763254
221
2.06796480059914
0.386482679689726
123
1.14791237595956
0.262106690721966
99
ABCD3|5825
8659
120.33055323881
30.1285604129915
11841
164.537948290242
32.1474762362659
27367
380.3113705866
50.1095795279887
...
7.4420570860444
2281
31.675562969141
6.75729552443108
8687
120.702529886016
22.5574354702822
9945
138.18682235196
31.4673320823522
100
ABCD4|5826
1153
23.5882834903728
5.91170299619709
2020
41.3621466612044
8.08132421677676
3424
70.0557148709545
9.23846846666413
...
6.73477305348576
929
19.0204834084392
4.05542150639004
2644
54.1376485047112
10.1170526793172
2023
41.4195002048341
9.43243187185178
100 rows × 2635 columns
In [9]:
r = DF['TCGA-A1-A0SB-01A-11R-A144-07.1'] # put the values of the column df to r
r
r = pd.to_numeric(r) # some values are different to numbers
In [8]:
DF.loc[56]
Out[8]:
Hybridization REF AASS|10157
TCGA-A1-A0SB-01A-11R-A144-07 1587
TCGA-A1-A0SB-01A-11R-A144-07.1 13.6199312714777
TCGA-A1-A0SB-01A-11R-A144-07.2 3.41275428968641
TCGA-A1-A0SD-01A-11R-A115-07 1852
TCGA-A1-A0SD-01A-11R-A115-07.1 15.9082474226804
TCGA-A1-A0SD-01A-11R-A115-07.2 3.10754150838332
TCGA-A1-A0SE-01A-11R-A084-07 2014
TCGA-A1-A0SE-01A-11R-A084-07.1 17.2955326460481
TCGA-A1-A0SE-01A-11R-A084-07.2 2.27913728420137
TCGA-A1-A0SF-01A-11R-A144-07 852
TCGA-A1-A0SF-01A-11R-A144-07.1 7.31769759450172
TCGA-A1-A0SF-01A-11R-A144-07.2 1.92001194799097
TCGA-A1-A0SG-01A-11R-A144-07 469
TCGA-A1-A0SG-01A-11R-A144-07.1 4.01821305841924
TCGA-A1-A0SG-01A-11R-A144-07.2 0.965129133618333
TCGA-A1-A0SH-01A-11R-A084-07 2278
TCGA-A1-A0SH-01A-11R-A084-07.1 19.5611683848797
TCGA-A1-A0SH-01A-11R-A084-07.2 2.42745579804307
TCGA-A1-A0SI-01A-11R-A144-07 884
TCGA-A1-A0SI-01A-11R-A144-07.1 7.57852233676976
TCGA-A1-A0SI-01A-11R-A144-07.2 1.63608714701755
TCGA-A1-A0SJ-01A-11R-A084-07 1547
TCGA-A1-A0SJ-01A-11R-A084-07.1 13.2850515463918
TCGA-A1-A0SJ-01A-11R-A084-07.2 1.86684109970372
TCGA-A1-A0SK-01A-12R-A084-07 829
TCGA-A1-A0SK-01A-12R-A084-07.1 7.09982817869416
TCGA-A1-A0SK-01A-12R-A084-07.2 0.905459617459822
TCGA-A1-A0SM-01A-11R-A084-07 1775
TCGA-A1-A0SM-01A-11R-A084-07.1 15.2378006872852
...
TCGA-EW-A2FW-01A-11R-A17B-07 1270
TCGA-EW-A2FW-01A-11R-A17B-07.1 10.9087628865979
TCGA-EW-A2FW-01A-11R-A17B-07.2 1.60102181647788
TCGA-GI-A2C8-11A-22R-A16F-07 1052
TCGA-GI-A2C8-11A-22R-A16F-07.1 9.02353951890034
TCGA-GI-A2C8-11A-22R-A16F-07.2 1.56854802119611
TCGA-GI-A2C8-01A-11R-A16F-07 901
TCGA-GI-A2C8-01A-11R-A16F-07.1 7.7340206185567
TCGA-GI-A2C8-01A-11R-A16F-07.2 1.43630182562309
TCGA-GM-A2D9-01A-11R-A18M-07 1001
TCGA-GM-A2D9-01A-11R-A18M-07.1 8.59553264604811
TCGA-GM-A2D9-01A-11R-A18M-07.2 2.05226584390785
TCGA-GM-A2DB-01A-31R-A18M-07 635
TCGA-GM-A2DB-01A-31R-A18M-07.1 5.45274914089347
TCGA-GM-A2DB-01A-31R-A18M-07.2 1.20379294122199
TCGA-GM-A2DC-01A-11R-A18M-07 628
TCGA-GM-A2DC-01A-11R-A18M-07.1 5.3946735395189
TCGA-GM-A2DC-01A-11R-A18M-07.2 1.0865469921428
TCGA-GM-A2DD-01A-11R-A180-07 684
TCGA-GM-A2DD-01A-11R-A180-07.1 5.87233676975945
TCGA-GM-A2DD-01A-11R-A180-07.2 1.35489093324684
TCGA-GM-A2DF-01A-11R-A180-07 483
TCGA-GM-A2DF-01A-11R-A180-07.1 4.14896907216495
TCGA-GM-A2DF-01A-11R-A180-07.2 0.884325628617842
TCGA-GM-A2DH-01A-11R-A180-07 792
TCGA-GM-A2DH-01A-11R-A180-07.1 6.80240549828179
TCGA-GM-A2DH-01A-11R-A180-07.2 1.27104971298882
TCGA-GM-A2DK-01A-21R-A180-07 940
TCGA-GM-A2DK-01A-21R-A180-07.1 8.07199312714777
TCGA-GM-A2DK-01A-21R-A180-07.2 1.8382325105988
Name: 56, dtype: object
In [10]:
# Genes = DF[DF['Hybridization REF'].isin(['?|100134869', 'ZSCAN20|7579'])]
Genes = DF.iloc[[2,3,56],range(3,879,3)]
Genes.head()
Out[10]:
TCGA-A1-A0SB-01A-11R-A144-07.2
TCGA-A1-A0SD-01A-11R-A115-07.2
TCGA-A1-A0SE-01A-11R-A084-07.2
TCGA-A1-A0SF-01A-11R-A144-07.2
TCGA-A1-A0SG-01A-11R-A144-07.2
TCGA-A1-A0SH-01A-11R-A084-07.2
TCGA-A1-A0SI-01A-11R-A144-07.2
TCGA-A1-A0SJ-01A-11R-A084-07.2
TCGA-A1-A0SK-01A-12R-A084-07.2
TCGA-A1-A0SM-01A-11R-A084-07.2
...
TCGA-AQ-A0Y5-01A-11R-A14M-07.2
TCGA-AQ-A1H2-01A-11R-A13Q-07.2
TCGA-AQ-A1H3-01A-31R-A13Q-07.2
TCGA-AR-A0TP-01A-11R-A084-07.2
TCGA-AR-A0TQ-01A-11R-A084-07.2
TCGA-AR-A0TR-01A-11R-A084-07.2
TCGA-AR-A0TS-01A-11R-A115-07.2
TCGA-AR-A0TT-01A-31R-A084-07.2
TCGA-AR-A0TU-01A-31R-A109-07.2
TCGA-AR-A0TV-01A-21R-A084-07.2
3
0.46324930208213
0.447232631700592
0.297493981144456
0.411404472217833
0.353138532837639
0.213990733730854
0.2027262981864
0.176242927790391
1.15251627209929
0.454509755110061
...
0.318428485692958
0.3122459931189
0.379084026833611
1.05832358119645
0.236873227868263
0.329944783872253
0.946653784516954
0.402321661789034
0.3074097245399
0.303718436945855
4
5.29354054052308
2.68707552797622
4.05941035836283
4.63994383524924
3.42728199800822
3.13017423359066
3.69212614304972
4.63801553840846
61.8986966406538
3.44495848697808
...
3.29417741207505
1.99837084915511
3.0771709075775
2.83609727372246
6.62110123937096
2.73248775618131
4.20436595839491
6.11002678582445
7.70457705843712
2.60354608704857
57
16.6449132292871
25.5951041505217
29.0610124819873
28.1091438397398
19.2747569511261
22.0398123645563
14.3254280880009
36.3693982922133
34.0314828601895
22.7884993660709
...
45.1846147036343
32.0177095086976
24.3608038337495
18.1811759760087
22.9593845992789
23.7275496335938
22.7253935620486
59.7106762336955
30.4058874396813
35.0459158691754
3 rows × 292 columns
In [11]:
Gene_3 = Genes.iloc[0]
Gene_4 = Genes.iloc[1]
Gene_5 = Genes.iloc[2]
Gene_3 = pd.to_numeric(Gene_3)
Gene_4 = pd.to_numeric(Gene_4)
Gene_5 = pd.to_numeric(Gene_5)
In [17]:
Gene_3
Out[17]:
TCGA-A1-A0SB-01A-11R-A144-07.2 0.463249
TCGA-A1-A0SD-01A-11R-A115-07.2 0.447233
TCGA-A1-A0SE-01A-11R-A084-07.2 0.297494
TCGA-A1-A0SF-01A-11R-A144-07.2 0.411404
TCGA-A1-A0SG-01A-11R-A144-07.2 0.353139
TCGA-A1-A0SH-01A-11R-A084-07.2 0.213991
TCGA-A1-A0SI-01A-11R-A144-07.2 0.202726
TCGA-A1-A0SJ-01A-11R-A084-07.2 0.176243
TCGA-A1-A0SK-01A-12R-A084-07.2 1.152516
TCGA-A1-A0SM-01A-11R-A084-07.2 0.454510
TCGA-A1-A0SN-01A-11R-A144-07.2 0.269296
TCGA-A1-A0SO-01A-22R-A084-07.2 0.688159
TCGA-A1-A0SP-01A-11R-A084-07.2 0.296785
TCGA-A1-A0SQ-01A-21R-A144-07.2 0.047078
TCGA-A2-A04N-01A-11R-A115-07.2 0.507076
TCGA-A2-A04P-01A-31R-A034-07.2 0.124894
TCGA-A2-A04Q-01A-21R-A034-07.2 0.148969
TCGA-A2-A04R-01A-41R-A109-07.2 0.567993
TCGA-A2-A04T-01A-21R-A034-07.2 0.663459
TCGA-A2-A04U-01A-11R-A115-07.2 0.046557
TCGA-A2-A04V-01A-21R-A034-07.2 0.218594
TCGA-A2-A04W-01A-31R-A115-07.2 0.127855
TCGA-A2-A04X-01A-21R-A034-07.2 0.152032
TCGA-A2-A04Y-01A-21R-A034-07.2 0.459839
TCGA-A2-A0CL-01A-11R-A115-07.2 0.454277
TCGA-A2-A0CM-01A-31R-A034-07.2 0.341826
TCGA-A2-A0CP-01A-11R-A034-07.2 0.259016
TCGA-A2-A0CQ-01A-21R-A034-07.2 0.193711
TCGA-A2-A0CS-01A-11R-A115-07.2 0.114043
TCGA-A2-A0CT-01A-31R-A056-07.2 0.201813
...
TCGA-AO-A125-01A-11R-A10J-07.2 0.344802
TCGA-AO-A126-01A-11R-A10J-07.2 0.135904
TCGA-AO-A128-01A-11R-A10J-07.2 0.294365
TCGA-AO-A129-01A-21R-A10J-07.2 0.312727
TCGA-AO-A12A-01A-21R-A115-07.2 0.581281
TCGA-AO-A12B-01A-11R-A10J-07.2 0.033265
TCGA-AO-A12C-01A-11R-A10J-07.2 0.461256
TCGA-AO-A12D-01A-11R-A115-07.2 0.301033
TCGA-AO-A12E-01A-11R-A10J-07.2 0.245424
TCGA-AO-A12F-01A-11R-A115-07.2 0.551958
TCGA-AO-A12G-01A-11R-A10J-07.2 0.045219
TCGA-AO-A12H-01A-11R-A115-07.2 0.075642
TCGA-AO-A1KO-01A-31R-A13Q-07.2 0.541354
TCGA-AO-A1KP-01A-11R-A13Q-07.2 0.347979
TCGA-AO-A1KR-01A-12R-A144-07.2 0.359247
TCGA-AO-A1KS-01A-11R-A13Q-07.2 0.615129
TCGA-AO-A1KT-01A-11R-A13Q-07.2 0.258507
TCGA-AQ-A04H-01B-11R-A10J-07.2 0.182700
TCGA-AQ-A04J-01A-02R-A034-07.2 0.663314
TCGA-AQ-A04L-01B-21R-A10J-07.2 0.290848
TCGA-AQ-A0Y5-01A-11R-A14M-07.2 0.318428
TCGA-AQ-A1H2-01A-11R-A13Q-07.2 0.312246
TCGA-AQ-A1H3-01A-31R-A13Q-07.2 0.379084
TCGA-AR-A0TP-01A-11R-A084-07.2 1.058324
TCGA-AR-A0TQ-01A-11R-A084-07.2 0.236873
TCGA-AR-A0TR-01A-11R-A084-07.2 0.329945
TCGA-AR-A0TS-01A-11R-A115-07.2 0.946654
TCGA-AR-A0TT-01A-31R-A084-07.2 0.402322
TCGA-AR-A0TU-01A-31R-A109-07.2 0.307410
TCGA-AR-A0TV-01A-21R-A084-07.2 0.303718
Name: 3, dtype: float64
In [19]:
sns.distplot(Gene_5)
Out[19]:
<matplotlib.axes._subplots.AxesSubplot at 0x11f3e6350>
In [16]:
sns.distplot(Gene_3)
sns.distplot(Gene_4)
sns.distplot(Gene_5)
Out[16]:
<matplotlib.axes._subplots.AxesSubplot at 0x11f081e50>
In [12]:
Genes = DF[DF['Hybridization REF'].isin(['TP53|7157', 'MDM2|4193', 'BRCA1|672'])]
Genes = Genes.set_index('Hybridization REF')
Genes = Genes.iloc[:,range(2,879,3)]
Genes
Out[12]:
TCGA-A1-A0SB-01A-11R-A144-07.2
TCGA-A1-A0SD-01A-11R-A115-07.2
TCGA-A1-A0SE-01A-11R-A084-07.2
TCGA-A1-A0SF-01A-11R-A144-07.2
TCGA-A1-A0SG-01A-11R-A144-07.2
TCGA-A1-A0SH-01A-11R-A084-07.2
TCGA-A1-A0SI-01A-11R-A144-07.2
TCGA-A1-A0SJ-01A-11R-A084-07.2
TCGA-A1-A0SK-01A-12R-A084-07.2
TCGA-A1-A0SM-01A-11R-A084-07.2
...
TCGA-AQ-A1H2-01A-11R-A13Q-07.2
TCGA-AQ-A1H3-01A-31R-A13Q-07.2
TCGA-AR-A0TP-01A-11R-A084-07.2
TCGA-AR-A0TQ-01A-11R-A084-07.2
TCGA-AR-A0TR-01A-11R-A084-07.2
TCGA-AR-A0TS-01A-11R-A115-07.2
TCGA-AR-A0TT-01A-31R-A084-07.2
TCGA-AR-A0TU-01A-31R-A109-07.2
TCGA-AR-A0TV-01A-21R-A084-07.2
TCGA-AR-A0TW-01A-11R-A084-07.2
Hybridization REF
BRCA1|672
4.40496
3.65636
5.37729
3.17787
4.2747
2.16336
5.00327
3.44012
12.6588
1.93891
...
2.49463
9.83356
0.604788
7.50332
3.03296
2.22486
3.65182
0.734913
9.10292
2.93352
MDM2|4193
16.6739
16.2067
15.2011
13.7754
38.3826
13.4172
10.8613
120.639
15.0297
13.3813
...
22.0235
16.7599
15.8524
20.4334
43.1792
13.8332
21.4815
10.14
13.553
21.8699
TP53|7157
125.101
38.8403
45.19
49.6044
48.7414
33.4708
49.6928
32.741
196.599
31.8967
...
26.781
38.98
49.8788
81.5742
27.325
24.3804
83.7166
131.187
43.6887
34.48
3 rows × 293 columns
In [17]:
for i, r in Genes.iterrows():
sns.distplot(r.values, label=i, axlabel= 'PATIENTS' )
sns.plt.legend()
Out[17]:
<matplotlib.legend.Legend at 0x1133a8650>
In [25]:
for i, r in Genes.iterrows():
sns.boxplot(r.values)
sns.plt.legend()
In [ ]:
In [ ]:
Content source: spulido99/Programacion
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