a b/tests/deseq2/test_vst.py 

  1
  
import unittest





  
  

  2
  





  
  

  3
  
import numpy as np





  
  

  4
  





  
  

  5
  
from inmoose.deseq2 import makeExampleDESeqDataSet, varianceStabilizingTransformation





  
  

  6
  





  
  

  7
  





  
  

  8
  
class Test(unittest.TestCase):





  
  

  9
  
    def test_varianceStabilizingTransform(self):





  
  

  10
  
        """check that variance StabilizingTransform works as expected"""





  
  

  11
  
        dds = makeExampleDESeqDataSet(n=15, m=12, seed=42)





  
  

  12
  
        vst = varianceStabilizingTransformation(dds)





  
  

  13
  





  
  

  14
  
        ref = np.array(





  
  

  15
  
            [





  
  

  16
  
                [





  
  

  17
  
                    3.823017,





  
  

  18
  
                    3.8230169,





  
  

  19
  
                    5.985321,





  
  

  20
  
                    4.913315,





  
  

  21
  
                    4.161231,





  
  

  22
  
                    1.494246,





  
  

  23
  
                    4.823440,





  
  

  24
  
                    5.450071,





  
  

  25
  
                    3.823017,





  
  

  26
  
                    1.3401978,





  
  

  27
  
                    3.595272,





  
  

  28
  
                    3.823017,





  
  

  29
  
                ],





  
  

  30
  
                [





  
  

  31
  
                    -0.451858,





  
  

  32
  
                    0.6581684,





  
  

  33
  
                    2.810054,





  
  

  34
  
                    1.254434,





  
  

  35
  
                    -0.451858,





  
  

  36
  
                    4.077032,





  
  

  37
  
                    -0.451858,





  
  

  38
  
                    -0.451858,





  
  

  39
  
                    4.086414,





  
  

  40
  
                    -0.4518580,





  
  

  41
  
                    1.546176,





  
  

  42
  
                    2.955590,





  
  

  43
  
                ],





  
  

  44
  
                [





  
  

  45
  
                    8.061588,





  
  

  46
  
                    6.3072368,





  
  

  47
  
                    4.637324,





  
  

  48
  
                    1.851704,





  
  

  49
  
                    4.161231,





  
  

  50
  
                    7.255872,





  
  

  51
  
                    0.824648,





  
  

  52
  
                    5.171055,





  
  

  53
  
                    5.671037,





  
  

  54
  
                    5.1710549,





  
  

  55
  
                    5.919773,





  
  

  56
  
                    8.977944,





  
  

  57
  
                ],





  
  

  58
  
                [





  
  

  59
  
                    4.243021,





  
  

  60
  
                    6.7404002,





  
  

  61
  
                    6.359506,





  
  

  62
  
                    2.576007,





  
  

  63
  
                    5.365497,





  
  

  64
  
                    5.015233,





  
  

  65
  
                    2.906480,





  
  

  66
  
                    8.951864,





  
  

  67
  
                    4.671504,





  
  

  68
  
                    5.9054920,





  
  

  69
  
                    6.892472,





  
  

  70
  
                    5.308661,





  
  

  71
  
                ],





  
  

  72
  
                [





  
  

  73
  
                    2.178302,





  
  

  74
  
                    -0.4518580,





  
  

  75
  
                    1.105434,





  
  

  76
  
                    -0.451858,





  
  

  77
  
                    1.395415,





  
  

  78
  
                    -0.451858,





  
  

  79
  
                    -0.451858,





  
  

  80
  
                    3.694642,





  
  

  81
  
                    3.500141,





  
  

  82
  
                    0.6253966,





  
  

  83
  
                    3.595272,





  
  

  84
  
                    -0.451858,





  
  

  85
  
                ],





  
  

  86
  
                [





  
  

  87
  
                    2.955590,





  
  

  88
  
                    -0.4518580,





  
  

  89
  
                    -0.451858,





  
  

  90
  
                    2.576007,





  
  

  91
  
                    1.847902,





  
  

  92
  
                    1.494246,





  
  

  93
  
                    0.824648,





  
  

  94
  
                    3.183966,





  
  

  95
  
                    3.500141,





  
  

  96
  
                    1.3401978,





  
  

  97
  
                    3.135366,





  
  

  98
  
                    4.359573,





  
  

  99
  
                ],





  
  

  100
  
                [





  
  

  101
  
                    -0.451858,





  
  

  102
  
                    3.3285650,





  
  

  103
  
                    1.664144,





  
  

  104
  
                    2.261056,





  
  

  105
  
                    1.641409,





  
  

  106
  
                    2.586723,





  
  

  107
  
                    4.623337,





  
  

  108
  
                    6.141930,





  
  

  109
  
                    -0.451858,





  
  

  110
  
                    -0.4518580,





  
  

  111
  
                    2.834227,





  
  

  112
  
                    6.598715,





  
  

  113
  
                ],





  
  

  114
  
                [





  
  

  115
  
                    4.359573,





  
  

  116
  
                    2.0207666,





  
  

  117
  
                    4.118937,





  
  

  118
  
                    1.851704,





  
  

  119
  
                    4.233253,





  
  

  120
  
                    2.920369,





  
  

  121
  
                    -0.451858,





  
  

  122
  
                    3.183966,





  
  

  123
  
                    2.057386,





  
  

  124
  
                    1.0399000,





  
  

  125
  
                    1.012888,





  
  

  126
  
                    4.359573,





  
  

  127
  
                ],





  
  

  128
  
                [





  
  

  129
  
                    2.178302,





  
  

  130
  
                    -0.4518580,





  
  

  131
  
                    -0.451858,





  
  

  132
  
                    6.038225,





  
  

  133
  
                    5.755725,





  
  

  134
  
                    3.416888,





  
  

  135
  
                    2.327658,





  
  

  136
  
                    3.183966,





  
  

  137
  
                    3.082433,





  
  

  138
  
                    3.9153624,





  
  

  139
  
                    5.408736,





  
  

  140
  
                    -0.451858,





  
  

  141
  
                ],





  
  

  142
  
                [





  
  

  143
  
                    3.226560,





  
  

  144
  
                    3.2613786,





  
  

  145
  
                    2.992774,





  
  

  146
  
                    3.553961,





  
  

  147
  
                    2.184300,





  
  

  148
  
                    1.494246,





  
  

  149
  
                    0.824648,





  
  

  150
  
                    -0.451858,





  
  

  151
  
                    -0.451858,





  
  

  152
  
                    1.0399000,





  
  

  153
  
                    3.264959,





  
  

  154
  
                    -0.451858,





  
  

  155
  
                ],





  
  

  156
  
                [





  
  

  157
  
                    5.249530,





  
  

  158
  
                    1.0834807,





  
  

  159
  
                    2.992774,





  
  

  160
  
                    3.925805,





  
  

  161
  
                    4.896815,





  
  

  162
  
                    6.210543,





  
  

  163
  
                    4.823440,





  
  

  164
  
                    6.519649,





  
  

  165
  
                    5.630417,





  
  

  166
  
                    -0.4518580,





  
  

  167
  
                    4.875050,





  
  

  168
  
                    7.268652,





  
  

  169
  
                ],





  
  

  170
  
                [





  
  

  171
  
                    4.749485,





  
  

  172
  
                    4.3272243,





  
  

  173
  
                    4.791961,





  
  

  174
  
                    5.117967,





  
  

  175
  
                    2.962466,





  
  

  176
  
                    4.791961,





  
  

  177
  
                    4.791961,





  
  

  178
  
                    4.367923,





  
  

  179
  
                    6.588150,





  
  

  180
  
                    5.6595787,





  
  

  181
  
                    4.791961,





  
  

  182
  
                    4.749485,





  
  

  183
  
                ],





  
  

  184
  
                [





  
  

  185
  
                    5.472762,





  
  

  186
  
                    2.3195612,





  
  

  187
  
                    3.154617,





  
  

  188
  
                    3.688910,





  
  

  189
  
                    4.896815,





  
  

  190
  
                    4.791961,





  
  

  191
  
                    4.163592,





  
  

  192
  
                    3.183966,





  
  

  193
  
                    2.816266,





  
  

  194
  
                    3.1140628,





  
  

  195
  
                    1.012888,





  
  

  196
  
                    6.972229,





  
  

  197
  
                ],





  
  

  198
  
                [





  
  

  199
  
                    3.650416,





  
  

  200
  
                    4.1161861,





  
  

  201
  
                    4.335770,





  
  

  202
  
                    6.507277,





  
  

  203
  
                    6.111061,





  
  

  204
  
                    8.069817,





  
  

  205
  
                    5.319135,





  
  

  206
  
                    5.736698,





  
  

  207
  
                    5.786454,





  
  

  208
  
                    -0.4518580,





  
  

  209
  
                    7.342527,





  
  

  210
  
                    7.587853,





  
  

  211
  
                ],





  
  

  212
  
                [





  
  

  213
  
                    4.910890,





  
  

  214
  
                    1.6362631,





  
  

  215
  
                    4.690736,





  
  

  216
  
                    6.817270,





  
  

  217
  
                    1.847902,





  
  

  218
  
                    6.556714,





  
  

  219
  
                    3.832819,





  
  

  220
  
                    3.694642,





  
  

  221
  
                    -0.451858,





  
  

  222
  
                    4.9890014,





  
  

  223
  
                    2.210771,





  
  

  224
  
                    4.116186,





  
  

  225
  
                ],





  
  

  226
  
            ]





  
  

  227
  
        )





  
  

  228
  





  
  

  229
  
        self.assertTrue(np.allclose(vst.X, ref.T, atol=2e-2))





  
  

  230
  





  
  

  231
  
        ref = np.array(





  
  

  232
  
            [





  
  

  233
  
                [





  
  

  234
  
                    3.701496,





  
  

  235
  
                    3.7014964,





  
  

  236
  
                    5.958395,





  
  

  237
  
                    4.8565583,





  
  

  238
  
                    4.0653149,





  
  

  239
  
                    0.8610695,





  
  

  240
  
                    4.7630157,





  
  

  241
  
                    5.411009,





  
  

  242
  
                    3.701496,





  
  

  243
  
                    0.6327990,





  
  

  244
  
                    3.4527199,





  
  

  245
  
                    3.701496,





  
  

  246
  
                ],





  
  

  247
  
                [





  
  

  248
  
                    -2.822746,





  
  

  249
  
                    -0.4959506,





  
  

  250
  
                    2.562285,





  
  

  251
  
                    0.5019767,





  
  

  252
  
                    -2.8227460,





  
  

  253
  
                    3.9753014,





  
  

  254
  
                    -2.8227460,





  
  

  255
  
                    -2.822746,





  
  

  256
  
                    3.985348,





  
  

  257
  
                    -2.8227460,





  
  

  258
  
                    0.9362035,





  
  

  259
  
                    2.732023,





  
  

  260
  
                ],





  
  

  261
  
                [





  
  

  262
  
                    8.055215,





  
  

  263
  
                    6.2857065,





  
  

  264
  
                    4.568530,





  
  

  265
  
                    1.3618038,





  
  

  266
  
                    4.0653149,





  
  

  267
  
                    7.2447271,





  
  

  268
  
                    -0.2002053,





  
  

  269
  
                    5.123623,





  
  

  270
  
                    5.637539,





  
  

  271
  
                    5.1236227,





  
  

  272
  
                    5.8915925,





  
  

  273
  
                    8.974568,





  
  

  274
  
                ],





  
  

  275
  
                [





  
  

  276
  
                    4.152433,





  
  

  277
  
                    6.7244620,





  
  

  278
  
                    6.338743,





  
  

  279
  
                    2.2835920,





  
  

  280
  
                    5.3240677,





  
  

  281
  
                    4.9623662,





  
  

  282
  
                    2.6750276,





  
  

  283
  
                    8.948426,





  
  

  284
  
                    4.604330,





  
  

  285
  
                    5.8770306,





  
  

  286
  
                    6.8781302,





  
  

  287
  
                    5.265561,





  
  

  288
  
                ],





  
  

  289
  
                [





  
  

  290
  
                    1.790356,





  
  

  291
  
                    -2.8227460,





  
  

  292
  
                    0.267767,





  
  

  293
  
                    -2.8227460,





  
  

  294
  
                    0.7155806,





  
  

  295
  
                    -2.8227460,





  
  

  296
  
                    -2.8227460,





  
  

  297
  
                    3.561685,





  
  

  298
  
                    3.347746,





  
  

  299
  
                    -0.5558881,





  
  

  300
  
                    3.4527199,





  
  

  301
  
                    -2.822746,





  
  

  302
  
                ],





  
  

  303
  
                [





  
  

  304
  
                    2.732023,





  
  

  305
  
                    -2.8227460,





  
  

  306
  
                    -2.822746,





  
  

  307
  
                    2.2835920,





  
  

  308
  
                    1.3566659,





  
  

  309
  
                    0.8610695,





  
  

  310
  
                    -0.2002053,





  
  

  311
  
                    2.993639,





  
  

  312
  
                    3.347746,





  
  

  313
  
                    0.6327990,





  
  

  314
  
                    2.9384128,





  
  

  315
  
                    4.276066,





  
  

  316
  
                ],





  
  

  317
  
                [





  
  

  318
  
                    -2.822746,





  
  

  319
  
                    3.1566484,





  
  

  320
  
                    1.103729,





  
  

  321
  
                    1.8953193,





  
  

  322
  
                    1.0717726,





  
  

  323
  
                    2.2965211,





  
  

  324
  
                    4.5538679,





  
  

  325
  
                    6.117780,





  
  

  326
  
                    -2.822746,





  
  

  327
  
                    -2.8227460,





  
  

  328
  
                    2.5906548,





  
  

  329
  
                    6.581130,





  
  

  330
  
                ],





  
  

  331
  
                [





  
  

  332
  
                    4.276066,





  
  

  333
  
                    1.5866643,





  
  

  334
  
                    4.020143,





  
  

  335
  
                    1.3618038,





  
  

  336
  
                    4.1420452,





  
  

  337
  
                    2.6911747,





  
  

  338
  
                    -2.8227460,





  
  

  339
  
                    2.993639,





  
  

  340
  
                    1.634489,





  
  

  341
  
                    0.1617874,





  
  

  342
  
                    0.1175492,





  
  

  343
  
                    4.276066,





  
  

  344
  
                ],





  
  

  345
  
                [





  
  

  346
  
                    1.790356,





  
  

  347
  
                    -2.8227460,





  
  

  348
  
                    -2.822746,





  
  

  349
  
                    6.0122710,





  
  

  350
  
                    5.7241411,





  
  

  351
  
                    3.2553183,





  
  

  352
  
                    1.9788499,





  
  

  353
  
                    2.993639,





  
  

  354
  
                    2.877997,





  
  

  355
  
                    3.8014500,





  
  

  356
  
                    5.3685344,





  
  

  357
  
                    -2.822746,





  
  

  358
  
                ],





  
  

  359
  
                [





  
  

  360
  
                    3.041855,





  
  

  361
  
                    3.0811437,





  
  

  362
  
                    2.774996,





  
  

  363
  
                    3.4072156,





  
  

  364
  
                    1.7980092,





  
  

  365
  
                    0.8610695,





  
  

  366
  
                    -0.2002053,





  
  

  367
  
                    -2.822746,





  
  

  368
  
                    -2.822746,





  
  

  369
  
                    0.1617874,





  
  

  370
  
                    3.0851780,





  
  

  371
  
                    -2.822746,





  
  

  372
  
                ],





  
  

  373
  
                [





  
  

  374
  
                    5.204619,





  
  

  375
  
                    0.2324742,





  
  

  376
  
                    2.774996,





  
  

  377
  
                    3.8127224,





  
  

  378
  
                    4.8394025,





  
  

  379
  
                    6.1875168,





  
  

  380
  
                    4.7630157,





  
  

  381
  
                    6.501071,





  
  

  382
  
                    5.595959,





  
  

  383
  
                    -2.8227460,





  
  

  384
  
                    4.8167596,





  
  

  385
  
                    7.257606,





  
  

  386
  
                ],





  
  

  387
  
                [





  
  

  388
  
                    4.685865,





  
  

  389
  
                    4.2418104,





  
  

  390
  
                    4.730196,





  
  

  391
  
                    5.0687489,





  
  

  392
  
                    2.7399816,





  
  

  393
  
                    4.7301962,





  
  

  394
  
                    4.7301962,





  
  

  395
  
                    4.284902,





  
  

  396
  
                    6.570435,





  
  

  397
  
                    5.6258120,





  
  

  398
  
                    4.7301962,





  
  

  399
  
                    4.685865,





  
  

  400
  
                ],





  
  

  401
  
                [





  
  

  402
  
                    5.434311,





  
  

  403
  
                    1.9687389,





  
  

  404
  
                    2.960316,





  
  

  405
  
                    3.5554177,





  
  

  406
  
                    4.8394025,





  
  

  407
  
                    4.7301962,





  
  

  408
  
                    4.0678339,





  
  

  409
  
                    2.993639,





  
  

  410
  
                    2.569582,





  
  

  411
  
                    2.9141319,





  
  

  412
  
                    0.1175492,





  
  

  413
  
                    6.958660,





  
  

  414
  
                ],





  
  

  415
  
                [





  
  

  416
  
                    3.513271,





  
  

  417
  
                    4.0172023,





  
  

  418
  
                    4.250864,





  
  

  419
  
                    6.4885385,





  
  

  420
  
                    6.0863872,





  
  

  421
  
                    8.0634801,





  
  

  422
  
                    5.2763471,





  
  

  423
  
                    5.704694,





  
  

  424
  
                    5.755538,





  
  

  425
  
                    -2.8227460,





  
  

  426
  
                    7.3320319,





  
  

  427
  
                    7.579001,





  
  

  428
  
                ],





  
  

  429
  
                [





  
  

  430
  
                    4.854038,





  
  

  431
  
                    1.0645175,





  
  

  432
  
                    4.624456,





  
  

  433
  
                    6.8021604,





  
  

  434
  
                    1.3566659,





  
  

  435
  
                    6.5386078,





  
  

  436
  
                    3.7121294,





  
  

  437
  
                    3.561685,





  
  

  438
  
                    -2.822746,





  
  

  439
  
                    4.9351593,





  
  

  440
  
                    1.8316982,





  
  

  441
  
                    4.017202,





  
  

  442
  
                ],





  
  

  443
  
            ]





  
  

  444
  
        )





  
  

  445
  





  
  

  446
  
        dds = makeExampleDESeqDataSet(n=15, m=12, seed=42)





  
  

  447
  
        vst = varianceStabilizingTransformation(dds, fitType="mean")





  
  

  448
  





  
  

  449
  
        self.assertTrue(np.allclose(vst.X, ref.T, atol=3e-2))