Repositorio del Broad Institute: https://gdac.broadinstitute.org Datos de cancer a nivel mundial (Acceso 4)
In [1]:
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[1]:
<matplotlib.axes._subplots.AxesSubplot at 0x1138f1ed0>
In [2]:
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')
DF
/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)
Out[2]:
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
0
gene
raw_counts
median_length_normalized
RPKM
raw_counts
median_length_normalized
RPKM
raw_counts
median_length_normalized
RPKM
...
RPKM
raw_counts
median_length_normalized
RPKM
raw_counts
median_length_normalized
RPKM
raw_counts
median_length_normalized
RPKM
1
?|100130426
0
0
0
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0
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0
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0
...
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2
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115
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1.19146690937079
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5.53890728476821
1.08327022136351
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4.85264900662252
0.648804765767191
...
0.496258123278805
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162
6.65894039735099
1.25258850027006
80
3.31043046357616
0.753734902894534
3
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In [21]:
DF = DF.drop([0]) # eliminar la prmiera fila
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-21-abcba4975a13> in <module>()
----> 1 DF = DF.drop([0]) # eliminar la prmiera fila
2
3 DF.loc[1]
/Users/camilogarcia/anaconda/lib/python2.7/site-packages/pandas/core/generic.pyc in drop(self, labels, axis, level, inplace, errors)
1905 new_axis = axis.drop(labels, level=level, errors=errors)
1906 else:
-> 1907 new_axis = axis.drop(labels, errors=errors)
1908 dropped = self.reindex(**{axis_name: new_axis})
1909 try:
/Users/camilogarcia/anaconda/lib/python2.7/site-packages/pandas/indexes/base.pyc in drop(self, labels, errors)
3260 if errors != 'ignore':
3261 raise ValueError('labels %s not contained in axis' %
-> 3262 labels[mask])
3263 indexer = indexer[~mask]
3264 return self.delete(indexer)
ValueError: labels [0] not contained in axis
In [4]:
DF.head()
Out[4]:
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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0.753734902894534
3
?|100134869
59
1.85069008782936
0.46324930208213
73
2.28983688833124
0.447232631700592
72
2.25846925972396
0.297493981144456
...
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
5 rows × 2635 columns
In [42]:
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
Out[42]:
1 0
2 4.7408940397351
3 1.85069008782936
4 21.1477987421384
5 85.8550983899821
6 0
7 17.2432804962095
8 0.827205882352941
9 0
10 0
11 0.128932439401753
12 0.0911386013632921
13 0.151057401812689
14 0
15 0.141435678749112
16 0
17 0
18 0
19 0
20 14.6589390142022
21 5.75635103926097
22 2.13533834586466
23 10.6299212598425
24 0
25 0
26 2.3393085787452
27 0
28 56.5437629221227
29 0.500230520977409
30 3.19088766692852
...
20503 4.74148
20504 19.0072
20505 5.65729
20506 6.87836
20507 20.2101
20508 65.3645
20509 0.110619
20510 8.18713
20511 0.307503
20512 25.434
20513 0
20514 7.71169
20515 24.161
20516 2.20307
20517 11.3334
20518 30.9771
20519 14.946
20520 35.023
20521 24.0899
20522 35.0421
20523 7.45149
20524 14.1453
20525 64.3016
20526 2.25372
20527 32.9284
20528 409.425
20529 94.7092
20530 71.3995
20531 93.5262
20532 0.825593
Name: TCGA-A1-A0SB-01A-11R-A144-07.1, dtype: object
In [68]:
DF.loc[56]
Out[68]:
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 [81]:
# Genes = DF[DF['Hybridization REF'].isin(['?|100134869', 'ZSCAN20|7579'])]
Genes = DF.iloc[[2,3,56],range(3,879,3)]
Genes
#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 [6]:
sns.distplot(r[r > 400])
Out[6]:
<matplotlib.axes._subplots.AxesSubplot at 0x11bb77d90>
In [82]:
sns.distplot(Gene_3)
sns.distplot(Gene_4)
sns.distplot(Gene_5)
Out[82]:
<matplotlib.axes._subplots.AxesSubplot at 0x11d03c2d0>
In [ ]:
Content source: spulido99/Programacion
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