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Calour Experiment class tutorial

Learn about how calour stores the data of an experiment

Setup





In [1]:



    


import calour as ca
ca.set_log_level(11)
import numpy as np
import matplotlib.pyplot as plt
%matplotlib notebook



    


















    






/Users/amnon/miniconda3/envs/calour/lib/python3.5/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
  from ._conv import register_converters as _register_converters

Load the data

we use the chronic fatigue syndrome data from:

Giloteaux, L., Goodrich, J.K., Walters, W.A., Levine, S.M., Ley, R.E. and Hanson, M.R., 2016.

Reduced diversity and altered composition of the gut microbiome in individuals with myalgic encephalomyelitis/chronic fatigue syndrome.

Microbiome, 4(1), p.30.





In [2]:



    


cfs=ca.read_amplicon('data/chronic-fatigue-syndrome.biom',
                     'data/chronic-fatigue-syndrome.sample.txt',
                     normalize=10000,min_reads=1000)



    


















    






2018-03-04 12:36:35 INFO loaded 87 samples, 2129 features
2018-03-04 12:36:35 WARNING These have metadata but do not have data - dropped: {'ERR1331814'}
2018-03-04 12:36:35 INFO After filtering, 87 remaining

The Experiment class

Calour stores the experiment as two Pandas.DataFrame (for sample_metadata and feature_metadata) and a (sparse or dense) data matrix.

The order in the dataframes and the table is synchronized, so entry number X in the sample_metadata dataframe always corresponds to row X in the data matrix (and similarily entry Y in the feature_metadata always corresponds to column Y in the data matrix).

The __repr__ of the Experiment

Contains the class (in our case - ca.AmpliconExperiment - which is derived from ca.Experiment),

the original biom table filename,

and how many samples and features does it have.





In [3]:



    


print(cfs)



    


















    






AmpliconExperiment ("chronic-fatigue-syndrome.biom") with 87 samples, 2129 features

The per-sample metadata (Experiment.sample_metadata)

This is a Pandas.DataFrame, with the index being the SampleID, and columns for the sample metadata fields (loaded from the mapping file).

Note that Calour also added the "_calour_original_abundance" field





In [4]:



    


cfs.sample_metadata



    


















    
Out[4]:











  
    

      
      BioSample_s
      Experiment_s
      MBases_l
      MBytes_l
      Run_s
      SRA_Sample_s
      Sample_Name_s
      Assay_Type_s
      AssemblyName_s
      BioProject_s
      ...
      Description
      Subject
      Emotional_well_being
      Role_physical
      Bell
      Physical_functioning
      Pain
      Age
      BMI
      _calour_original_abundance
    

    

      #SampleID
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
    

  
  
    

      ERR1331798
      SAMEA3904128
      ERX1403418
      43
      29
      ERR1331798
      ERS1091262
      LR16
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Patient
      72.0
      0.0
      20.0
      75.0
      23.0
      50
      37.59
      62629.0
    

    

      ERR1331812
      SAMEA3904142
      ERX1403432
      77
      54
      ERR1331812
      ERS1091276
      LR72
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Patient
      56.0
      NaN
      30.0
      60.0
      68.0
      64
      22.85
      96404.0
    

    

      ERR1331836
      SAMEA3904166
      ERX1403456
      83
      56
      ERR1331836
      ERS1091300
      LR42
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Control
      NaN
      NaN
      NaN
      NaN
      NaN
      35
      30.66
      105470.0
    

    

      ERR1331831
      SAMEA3904161
      ERX1403451
      38
      26
      ERR1331831
      ERS1091295
      IC10
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Control
      NaN
      NaN
      NaN
      NaN
      NaN
      45
      22.24
      50560.0
    

    

      ERR1331815
      SAMEA3904145
      ERX1403435
      49
      33
      ERR1331815
      ERS1091279
      LR75
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Patient
      NaN
      NaN
      NaN
      NaN
      NaN
      41
      32.30
      66414.0
    

    

      ERR1331870
      SAMEA3904200
      ERX1403490
      61
      42
      ERR1331870
      ERS1091334
      LR31
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Patient
      72.0
      0.0
      NaN
      0.0
      20.0
      50
      21.96
      97011.0
    

    

      ERR1331791
      SAMEA3904121
      ERX1403411
      52
      35
      ERR1331791
      ERS1091255
      LR08
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Patient
      50.0
      0.0
      10.0
      45.0
      10.0
      45
      25.23
      77673.0
    

    

      ERR1331854
      SAMEA3904184
      ERX1403474
      46
      31
      ERR1331854
      ERS1091318
      LR51
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Control
      NaN
      NaN
      NaN
      NaN
      NaN
      46
      28.34
      59655.0
    

    

      ERR1331853
      SAMEA3904183
      ERX1403473
      73
      48
      ERR1331853
      ERS1091317
      IC21
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Patient
      56.0
      0.0
      20.0
      40.0
      33.0
      34
      25.70
      100206.0
    

    

      ERR1331838
      SAMEA3904168
      ERX1403458
      24
      16
      ERR1331838
      ERS1091302
      LR40
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Patient
      8.0
      0.0
      50.0
      50.0
      23.0
      27
      26.47
      34044.0
    

    

      ERR1331796
      SAMEA3904126
      ERX1403416
      55
      38
      ERR1331796
      ERS1091260
      LR15
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Patient
      68.0
      0.0
      50.0
      35.0
      58.0
      43
      23.49
      74744.0
    

    

      ERR1331820
      SAMEA3904150
      ERX1403440
      66
      44
      ERR1331820
      ERS1091284
      IC06
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Control
      NaN
      NaN
      NaN
      NaN
      NaN
      47
      24.36
      106959.0
    

    

      ERR1331804
      SAMEA3904134
      ERX1403424
      53
      35
      ERR1331804
      ERS1091268
      LR69
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Patient
      48.0
      0.0
      20.0
      25.0
      33.0
      50
      17.70
      75014.0
    

    

      ERR1331868
      SAMEA3904198
      ERX1403488
      41
      27
      ERR1331868
      ERS1091332
      LR33
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Patient
      88.0
      0.0
      20.0
      5.0
      10.0
      64
      16.30
      64515.0
    

    

      ERR1331789
      SAMEA3904119
      ERX1403409
      36
      24
      ERR1331789
      ERS1091253
      LR04
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Patient
      64.0
      25.0
      50.0
      75.0
      45.0
      53
      24.03
      52549.0
    

    

      ERR1331803
      SAMEA3904133
      ERX1403423
      35
      23
      ERR1331803
      ERS1091267
      LR80
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Patient
      12.0
      0.0
      30.0
      35.0
      35.0
      52
      23.80
      54079.0
    

    

      ERR1331827
      SAMEA3904157
      ERX1403447
      28
      19
      ERR1331827
      ERS1091291
      IC15
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Control
      NaN
      NaN
      NaN
      NaN
      NaN
      48
      25.92
      41310.0
    

    

      ERR1331842
      SAMEA3904172
      ERX1403462
      44
      29
      ERR1331842
      ERS1091306
      LR24
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Control
      NaN
      NaN
      NaN
      NaN
      NaN
      54
      27.19
      66931.0
    

    

      ERR1331829
      SAMEA3904159
      ERX1403449
      46
      31
      ERR1331829
      ERS1091293
      IC12
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Control
      NaN
      NaN
      NaN
      NaN
      NaN
      24
      21.52
      69574.0
    

    

      ERR1331787
      SAMEA3904117
      ERX1403407
      52
      36
      ERR1331787
      ERS1091251
      LR01
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Patient
      32.0
      0.0
      40.0
      25.0
      0.0
      50
      24.89
      70387.0
    

    

      ERR1331866
      SAMEA3904196
      ERX1403486
      67
      45
      ERR1331866
      ERS1091330
      LR35
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Patient
      56.0
      0.0
      20.0
      15.0
      0.0
      19
      27.44
      93480.0
    

    

      ERR1331861
      SAMEA3904191
      ERX1403481
      63
      43
      ERR1331861
      ERS1091325
      LR56
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Patient
      68.0
      0.0
      20.0
      40.0
      33.0
      60
      23.57
      84020.0
    

    

      ERR1331845
      SAMEA3904175
      ERX1403465
      25
      17
      ERR1331845
      ERS1091309
      LR27
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Patient
      64.0
      75.0
      90.0
      95.0
      90.0
      48
      21.45
      40701.0
    

    

      ERR1331797
      SAMEA3904127
      ERX1403417
      52
      36
      ERR1331797
      ERS1091261
      LR17
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Patient
      52.0
      0.0
      40.0
      40.0
      23.0
      67
      32.89
      61849.0
    

    

      ERR1331839
      SAMEA3904169
      ERX1403459
      91
      62
      ERR1331839
      ERS1091303
      LR41
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Patient
      16.0
      0.0
      40.0
      55.0
      68.0
      50
      25.18
      119409.0
    

    

      ERR1331852
      SAMEA3904182
      ERX1403472
      37
      25
      ERR1331852
      ERS1091316
      IC20
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Control
      92.0
      100.0
      NaN
      100.0
      90.0
      34
      25.20
      51815.0
    

    

      ERR1331855
      SAMEA3904185
      ERX1403475
      42
      28
      ERR1331855
      ERS1091319
      LR50
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Control
      NaN
      NaN
      NaN
      NaN
      NaN
      42
      17.41
      59722.0
    

    

      ERR1331871
      SAMEA3904201
      ERX1403491
      32
      22
      ERR1331871
      ERS1091335
      LR30
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Patient
      80.0
      0.0
      40.0
      35.0
      45.0
      59
      21.61
      47760.0
    

    

      ERR1331790
      SAMEA3904120
      ERX1403410
      67
      44
      ERR1331790
      ERS1091254
      LR05
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Patient
      32.0
      0.0
      20.0
      20.0
      23.0
      51
      20.98
      101434.0
    

    

      ERR1331830
      SAMEA3904160
      ERX1403450
      67
      47
      ERR1331830
      ERS1091294
      IC11
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Control
      NaN
      NaN
      NaN
      NaN
      NaN
      36
      30.13
      85726.0
    

    

      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
    

    

      ERR1331851
      SAMEA3904181
      ERX1403471
      73
      50
      ERR1331851
      ERS1091315
      LR29
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Patient
      48.0
      0.0
      40.0
      35.0
      45.0
      62
      26.62
      92925.0
    

    

      ERR1331856
      SAMEA3904186
      ERX1403476
      18
      12
      ERR1331856
      ERS1091320
      LR53
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Patient
      92.0
      0.0
      50.0
      65.0
      90.0
      63
      30.54
      22203.0
    

    

      ERR1331872
      SAMEA3904202
      ERX1403492
      45
      31
      ERR1331872
      ERS1091336
      LR38
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Control
      NaN
      NaN
      NaN
      NaN
      NaN
      50
      24.89
      63500.0
    

    

      ERR1331793
      SAMEA3904123
      ERX1403413
      44
      29
      ERR1331793
      ERS1091257
      LR52
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Patient
      88.0
      0.0
      50.0
      65.0
      68.0
      33
      22.86
      64368.0
    

    

      ERR1331819
      SAMEA3904149
      ERX1403439
      55
      37
      ERR1331819
      ERS1091283
      IC05
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Control
      NaN
      NaN
      NaN
      NaN
      NaN
      33
      21.77
      73568.0
    

    

      ERR1331817
      SAMEA3904147
      ERX1403437
      47
      32
      ERR1331817
      ERS1091281
      IC09
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Control
      NaN
      NaN
      NaN
      NaN
      NaN
      55
      46.86
      69072.0
    

    

      ERR1331858
      SAMEA3904188
      ERX1403478
      63
      43
      ERR1331858
      ERS1091322
      LR55
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Control
      NaN
      NaN
      NaN
      NaN
      NaN
      48
      25.06
      89176.0
    

    

      ERR1331833
      SAMEA3904163
      ERX1403453
      48
      32
      ERR1331833
      ERS1091297
      LR47
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Control
      NaN
      NaN
      NaN
      NaN
      NaN
      54
      28.19
      64426.0
    

    

      ERR1331834
      SAMEA3904164
      ERX1403454
      43
      30
      ERR1331834
      ERS1091298
      LR44
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Control
      NaN
      NaN
      NaN
      NaN
      NaN
      49
      41.40
      59181.0
    

    

      ERR1331810
      SAMEA3904140
      ERX1403430
      74
      51
      ERR1331810
      ERS1091274
      LR78
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Patient
      84.0
      88.0
      40.0
      40.0
      0.0
      63
      24.53
      100251.0
    

    

      ERR1331823
      SAMEA3904153
      ERX1403443
      54
      37
      ERR1331823
      ERS1091287
      IC19
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Control
      NaN
      NaN
      NaN
      NaN
      NaN
      43
      26.15
      76190.0
    

    

      ERR1331848
      SAMEA3904178
      ERX1403468
      58
      39
      ERR1331848
      ERS1091312
      LR22
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Patient
      56.0
      100.0
      50.0
      70.0
      65.0
      56
      22.24
      84987.0
    

    

      ERR1331807
      SAMEA3904137
      ERX1403427
      50
      34
      ERR1331807
      ERS1091271
      LR65
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Patient
      88.0
      0.0
      20.0
      25.0
      10.0
      54
      29.95
      68514.0
    

    

      ERR1331800
      SAMEA3904130
      ERX1403420
      65
      44
      ERR1331800
      ERS1091264
      LR10
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Patient
      76.0
      25.0
      20.0
      40.0
      60.0
      61
      25.06
      84449.0
    

    

      ERR1331824
      SAMEA3904154
      ERX1403444
      59
      40
      ERR1331824
      ERS1091288
      IC18
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Control
      NaN
      NaN
      NaN
      NaN
      NaN
      48
      34.15
      80196.0
    

    

      ERR1331841
      SAMEA3904171
      ERX1403461
      38
      27
      ERR1331841
      ERS1091305
      LR49
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Control
      NaN
      NaN
      NaN
      NaN
      NaN
      60
      30.89
      48256.0
    

    

      ERR1331865
      SAMEA3904195
      ERX1403485
      36
      24
      ERR1331865
      ERS1091329
      LR36
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Control
      NaN
      NaN
      NaN
      NaN
      NaN
      20
      20.80
      47898.0
    

    

      ERR1331809
      SAMEA3904139
      ERX1403429
      41
      28
      ERR1331809
      ERS1091273
      LR79
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Patient
      56.0
      0.0
      20.0
      6.0
      45.0
      53
      28.34
      55874.0
    

    

      ERR1331862
      SAMEA3904192
      ERX1403482
      74
      51
      ERR1331862
      ERS1091326
      IC3
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Control
      NaN
      NaN
      NaN
      NaN
      NaN
      52
      21.79
      107258.0
    

    

      ERR1331846
      SAMEA3904176
      ERX1403466
      84
      57
      ERR1331846
      ERS1091310
      LR20
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Patient
      92.0
      50.0
      60.0
      40.0
      45.0
      71
      20.94
      110218.0
    

    

      ERR1331811
      SAMEA3904141
      ERX1403431
      43
      29
      ERR1331811
      ERS1091275
      LR73
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Patient
      36.0
      25.0
      50.0
      50.0
      33.0
      39
      28.66
      63968.0
    

    

      ERR1331835
      SAMEA3904165
      ERX1403455
      76
      52
      ERR1331835
      ERS1091299
      LR45
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Control
      NaN
      NaN
      NaN
      NaN
      NaN
      50
      23.43
      94907.0
    

    

      ERR1331832
      SAMEA3904162
      ERX1403452
      37
      25
      ERR1331832
      ERS1091296
      LR46
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Patient
      72.0
      0.0
      30.0
      56.0
      23.0
      65
      37.20
      49032.0
    

    

      ERR1331859
      SAMEA3904189
      ERX1403479
      53
      36
      ERR1331859
      ERS1091323
      LR54
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Patient
      76.0
      0.0
      30.0
      15.0
      10.0
      63
      25.79
      77150.0
    

    

      ERR1331816
      SAMEA3904146
      ERX1403436
      59
      40
      ERR1331816
      ERS1091280
      LR74
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Patient
      64.0
      25.0
      30.0
      50.0
      NaN
      51
      24.39
      89870.0
    

    

      ERR1331818
      SAMEA3904148
      ERX1403438
      54
      38
      ERR1331818
      ERS1091282
      IC04
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Control
      NaN
      NaN
      NaN
      NaN
      NaN
      32
      32.98
      71017.0
    

    

      ERR1331792
      SAMEA3904122
      ERX1403412
      32
      22
      ERR1331792
      ERS1091256
      LR09
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Control
      24.0
      100.0
      90.0
      80.0
      65.0
      43
      22.14
      41598.0
    

    

      ERR1331857
      SAMEA3904187
      ERX1403477
      61
      42
      ERR1331857
      ERS1091321
      IC8
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Control
      NaN
      NaN
      NaN
      NaN
      NaN
      53
      29.02
      89919.0
    

    

      ERR1331850
      SAMEA3904180
      ERX1403470
      54
      36
      ERR1331850
      ERS1091314
      LR28
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Control
      60.0
      75.0
      NaN
      80.0
      90.0
      50
      29.65
      72977.0
    

    

      ERR1331795
      SAMEA3904125
      ERX1403415
      56
      38
      ERR1331795
      ERS1091259
      LR18
      AMPLICON
      <not provided>
      PRJEB13092
      ...
      NaN
      Patient
      88.0
      0.0
      20.0
      55.0
      55.0
      62
      24.39
      80308.0
    

  



87 rows × 59 columns

The per-feature metadata (Experiment.feature_metadata)

This is a Pandas.DataFrame, with the index being the featureID (usually the sequence), and columns for the feature metadata (usually "taxonomy", and also additional fields added by calour following differential abundance testing)





In [5]:



    


cfs.feature_metadata



    


















    
Out[5]:











  
    

      
      taxonomy
    

  
  
    

      TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGACGCTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGGTGTCTTGAGTACAGTAGAGGCAGGCGGAATTCGTGG
      k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o_...
    

    

      TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGG
      k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o_...
    

    

      TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTGCGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTGGAAACTGTCGTACTTGAGTATCGGAGAGGTAAGTGGAATTCCTAG
      k__Bacteria;p__Firmicutes;c__Clostridia;o__Clo...
    

    

      TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGG
      k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o_...
    

    

      TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGG
      k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o_...
    

    

      TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGG
      k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o_...
    

    

      TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGG
      k__Bacteria;p__Proteobacteria;c__Gammaproteoba...
    

    

      AACGTAGGGTGCAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGACCGGCAAGTTGGAAGTGAAAACTATGGGCTCAACCCATAAATTGCTTTCAAAACTGCTGGCCTTGAGTAGTGCAGAGGTAGGTGGAATTCCCGG
      k__Bacteria;p__Firmicutes;c__Clostridia;o__Clo...
    

    

      AACGTAGGGTGCAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAAACCATGGGCTCAACCCATGAATTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGATGGAATTCCCGG
      k__Bacteria;p__Firmicutes;c__Clostridia;o__Clo...
    

    

      TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCAGTCTTGAGTGCAGTAGAGGTGGGCGGAATTCGTGG
      k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o_...
    

    

      AACGTAGGTCACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGG
      k__Bacteria;p__Firmicutes;c__Clostridia;o__Clo...
    

    

      TACGTAGGGGGCGAGCGTTGTCCGGAATGATTGGGCGTAAAGGGCGTGTAGGCGGCTTTATAAGTCTGGAGTGAAAGTCCTGTTTTCAAGATGGGAATTGCTTTGGATACTGTAGGGCTTGAGTGCAGGAGAGGTTATCGGAATTCCCGG
      k__Bacteria;p__Firmicutes;c__Clostridia;o__Clo...
    

    

      TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCGCAGCAAGTCTGATGTGAAAGGCAGGGGCTTAACCCCTGGACTGCATTGGAAACTGCTGTGCTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAG
      k__Bacteria;p__Firmicutes;c__Clostridia;o__Clo...
    

    

      TACGGAGGATGCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCACGCCAAGTCAGCGGTGAAATTTCCGGGCTCAACCCGGAGTGTGCCGTTGAAACTGGCGAGCTAGAGTACACAAGAGGCAGGCGGAATGCGTGG
      k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o_...
    

    

      TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGCATGATAAGTCTGATGTGAAAACCCAAGGCTCAACCATGGGACTGCATTGGAAACTGTCGTGCTGGAGTGTCGGAGAGGTGAGCGGAATTCCTAG
      k__Bacteria;p__Firmicutes;c__Clostridia;o__Clo...
    

    

      TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGCATGATAAGTCTGATGTGAAAACCCAAGGCTCAACCATGGGACTGCATTGGAAACTGTCGTGCTGGAGTGTCGGAGAGGTAAGCGGAATTCCTAG
      k__Bacteria;p__Firmicutes;c__Clostridia;o__Clo...
    

    

      TACGTAGGTGGCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGCGTGTAGGCGGAGCTGCAAGTCAGATGTGAAATCTCTGGGCTCAACCCAGAAACTGCATTTGAAACTGTAGCCCTTGAGTATCGGAGAGGCAAGCGGAATTCCTAG
      k__Bacteria;p__Firmicutes;c__Clostridia;o__Clo...
    

    

      TACGTAGGTCCCGAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTGATAAGTCTGAAGTTAAAGGCTGTGGCTCAACCATAGTTCGCTTTGGAAACTGTCAAACTTGAGTGCAGAAGGGGAGAGTGGAATTCCATGT
      k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactob...
    

    

      TACGTAGGGAGCGAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGTAGGCGGGATAGCAAGTCAGATGTGAAAACTATGGGCTCAACCTGTAGATTGCATTTGAAACTGTTGTTCTTGAGTGAAGTAGAGGTAAGCGGAATTCCTAG
      k__Bacteria;p__Firmicutes;c__Clostridia;o__Clo...
    

    

      TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGACTGGCAAGTCTGATGTGAAAGGCGGGGGCTCAACCCCTGGACTGCATTGGAAACTGTTAGTCTTGAGTGCCGGAGAGGTAAGCGGAATTCCTAG
      k__Bacteria;p__Firmicutes;c__Clostridia;o__Clo...
    

    

      TACGGAAGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGCTTTTAAGTCAGCGGTCAAATGTCACGGCTCAACCGTGGCCAGCCGTTGAAACTGTAAGCCTTGAGTCTGCACAGGGCACATGGAATTCGTGGT
      k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o_...
    

    

      TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAG
      k__Bacteria;p__Firmicutes;c__Clostridia;o__Clo...
    

    

      TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCACGCCAAGTCAGCGGTGAAATTTCCGGGCTCAACCCGGAGTGTGCCGTTGAAACTGGCGAGCTAGAGTACACAAGAGGCAGGCGGAATGCGTGG
      k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o_...
    

    

      TACGTAGGTGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGTGTAGGCGGGAGTGCAAGTCAGATGTGAAAACTATGGGCTCAACCCATAGCCTGCATTTGAAACTGTACTTCTTGAGTGATGGAGAGGCAGGCGGAATTCCCTG
      k__Bacteria;p__Firmicutes;c__Clostridia;o__Clo...
    

    

      TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGTGGTGATTTAAGTCAGCGGTGAAAGTTTGTGGCTCAACCATAAAATTGCCGTTGAAACTGGGTTACTTGAGTGTGTTTGAGGTAGGCGGAATGCGTGG
      k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o_...
    

    

      TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGGAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGG
      k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o_...
    

    

      TACGTAGGTGGCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGCGTGCAGCCGGGCATGCAAGTCAGATGTGAAATCTCAGGGCTTAACCCTGAAACTGCATTTGAAACTGTATGTCTTGAGTGCCGGAGAGGTAATCGGAATTCCTTG
      k__Bacteria;p__Firmicutes;c__Clostridia;o__Clo...
    

    

      TACGTAGGGAGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGCAGGCGGGCCGGTAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGCTGGTCTTGAGTGATGGAGAGGCAGGCGGAATTCCGTG
      k__Bacteria;p__Firmicutes;c__Clostridia;o__Clo...
    

    

      TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCACGGCAAGCCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGGAACTGCTGAGCTAGAGTGTCGGAGAGGCAAGTGGAATTCCTAG
      k__Bacteria;p__Firmicutes;c__Clostridia;o__Clo...
    

    

      TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGATGGGCAAGTCTGATGTGAAAACCCGGGGCTCAACCCCGGGACTGCATTGGAAACTGTTCATCTAGAGTGCTGGAGAGGTAAGTGGAATTCCTAG
      k__Bacteria;p__Firmicutes;c__Clostridia;o__Clo...
    

    

      ...
      ...
    

    

      TACGGAAGGTCCAGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGCAGGCGGACCTTTAAGTCAGCTGTGAAATACGGCGGCTCAACCGTCGAACTGCAGTTGATACTGGAGGTCTTGAGTGCACACAGGGATACTGGAATTCATGG
      k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o_...
    

    

      TACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCCGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGT
      k__Bacteria;p__Firmicutes;c__Clostridia;o__Clo...
    

    

      TACGTAGGTGGCGAGCGTTATCCGGAATCATTGGGCGTAAAGAGGGAGCAGGCGGCCGCAAGGGTCTGTGGTGAAAGACCGAAGCTAAACTTCGGTGAGCCATGGAAACCGGGCGGCTAGAGTGCGGAAGAGGATCGTGGAATTCCATGT
      k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o...
    

    

      TACGTAGGTGGCGAGCGTTATCCGGAATGATTGGGCGTAAAGGGTACGTAGGCGGCATGATAAGTCTGGAGTGAAAGGCTACAGCTCAACTGTAGTATGCTCTGGAAACTGTCAAGCTAGAGTGCAGAAGAGGGCAATGGAACTCCATGT
      k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o...
    

    

      TACGGAAGGTCCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGCGGGTTAAGCGTGTTGTGAAATGTAGGGGCTCAACCTCTGCACTGCAGCGCGAACTGGCTTGCTTGAGTACGCACAACGTGGGCGGAATTCGTGG
      k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o_...
    

    

      TACGGAAGGTCCAGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGCAGGCGGACCTTTAAGTCAGCTGTGAAATACGGCGGCTCAACCGTCGAACTGCAGTTGATACTGGAGGTCTTGAGTGCACACAGGGGTACTGGAATTCATGG
      k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o_...
    

    

      TACGTATGGAGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGTGTAGGTGGCCATGCAAGTCAGAAGTGAAAATCCGGGGCTCAACCTCGGAACTGCTTTTGAAACTGTAAGGCTGGAGTGCAGGAGGGGTGAGTGGAATTCCTAG
      k__Bacteria;p__Firmicutes;c__Clostridia;o__Clo...
    

    

      TACGGAAGGTCCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTGAGGTAAGCGTGTTGTGAAATGTAGGCGCCCAACGTCTGCACTGCAGCGCGAACTGCCCCACTTGAGTGTGCGCAACGCCGGCGGAACTCGTCG
      k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o_...
    

    

      TACGGAAGGTCCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTCTGTTAAGCGTGTTGTGAAATGTCGGGGCTCAACCTGGGCATTGCAGCGCGAACTGGCAGACTTGAGTGCACGGGAAGTAGGCGGAATTCGTCG
      k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o_...
    

    

      TACGTAGGTGGCGAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGTAGGCGGGAATGCAAGTCAGATGTGAAATCCAAGGGCTCAACCCTTGAACTGCATTTGAAACTGCATTTCTTGAGTGTCGGAGAGGTTGACGGAATTCCTAG
      k__Bacteria;p__Firmicutes;c__Clostridia;o__Clo...
    

    

      TACGTAGGTGGCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGCGTGTAGCCGGGTCGGCAAGTCAGATGTGAAATCTATGGGCTCAACTCATAAACTGCATTTGAAACTGTTGATCTTGAGTATCGGAGAGGCAATCGGAATTCCTAG
      k__Bacteria;p__Firmicutes;c__Clostridia;o__Clo...
    

    

      TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGACTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATCGCAGTTGATACTGGCAGTCTTGAGTACAGCAGAGGTGGGCGGAATTCGTGG
      k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o_...
    

    

      TACGTATGGGGCGAGCGTTATCCGGATTCATTGGGCGTAAAGCGCGCGTAGGCGGCCTGGCAGGCCGGGAGTCAAATCCGGGGGCTCAACCCCCGCCCGCTCCCGGAACCTTTAGGCTTGAGTCTGGCAGGGGAGGGTGGAATACCCGGT
      k__Bacteria;p__Actinobacteria;c__Coriobacterii...
    

    

      TACGTAGGGAGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGCAGGTGGGCCGGTAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGCTGGTCTTGAGTGATGGAGAGGCAGGCGGAATTCCGTG
      k__Bacteria;p__Firmicutes;c__Clostridia;o__Clo...
    

    

      TACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCCGTGCAAGTCCATCTTAAAAGCGTGGGGCTTAACCCCATGAGGGGATGGAAACTGCATGGCTGGAGTGTCGGAGGGGAAAGTGGAATTCCTAGT
      k__Bacteria;p__Firmicutes;c__Clostridia;o__Clo...
    

    

      TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTTAACCGTAAAATTGCAGTTGATACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGG
      k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o_...
    

    

      TACGTAGGTGACAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGCGCGTAGGCGGACTATCAAGTCAGTCGTGAAATACCGGGGCTTAACCCCGGGGCTGCGATTGAAACTGACAGCCTTGAGTATCGGAGAGGAAAGCGGAATTCCTAG
      k__Bacteria;p__Firmicutes;c__Clostridia;o__Clo...
    

    

      TACGGAGGGTGTAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGG
      k__Bacteria;p__Proteobacteria;c__Gammaproteoba...
    

    

      TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAATCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGG
      k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o_...
    

    

      TACGTAGGGGGCAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGAGAAGCAAGTCAGTGGTGAAAGGTATGGGCTTAACCCATAGACTGCCATTGAAACTGTTTTCCTTGAGTGAAGTAGAGGCAGGCGGAATTCCGAG
      k__Bacteria;p__Firmicutes;c__Clostridia;o__Clo...
    

    

      TACGTATGGAGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGGCGGTGCTGCAAGTCTGATGTGAAAACCCGGGGCTCAACCCCGGGACTGCATTGGAAACTGTAGGACTAGAGTGTCGGAGGGGTAAGTGGAATTCCTAG
      k__Bacteria;p__Firmicutes;c__Clostridia;o__Clo...
    

    

      TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGAGCAGCAAGTCTGATGTGAAAGGCGGGGGCTCAACCCCCCGGACTGCATTGGAAACTGTTGATCTTGAGTACCGGAGAGGTAAGCGGAATTCCTA
      k__Bacteria;p__Firmicutes;c__Clostridia;o__Clo...
    

    

      TACGTATGGAGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGTGTAGGTGGTCATGCAAGTCAGAAGTGAAAATCTGGGGCTCAACCCCGGAACTGCTTTTGAAACTGTAAGGCTGGAGTGCAGGAGGGGTGAGTGGAATTCCTAG
      k__Bacteria;p__Firmicutes;c__Clostridia;o__Clo...
    

    

      TACGTATGGAGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGTGTAGGTGGCCAGGCAAGTCAGAAGTGAAAGCCCAGGGCTCAACCCCGGGACTGCTTTTGAAACTGCAGGGCTAGAGTGCAGGAGGGGCAAGTGGAATTCCTAG
      k__Bacteria;p__Firmicutes;c__Clostridia;o__Clo...
    

    

      CACGGGGGATGCGAGCGTTATCCGGATTCATTGGGTTTAAAGGGAGCGTAGGCGGCCCGACAAGTCAGCGGTAAAAGACTGCAGCTAAACTGTAGCGCGCCGTTGAAACTGCCGGGCTCGAGTGCAGACGAGGTTGGCGGAACAGGTGAA
      k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o_...
    

    

      TACGTAGGGAGCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGATTGGCAAGTCAGAAGTGAAATCCATGGGCTTAACCCATGAACTGCTTTTGAAACTGTTAGTCTTGAGTGAAGCAGAGGTAGGCGGAATTCCCGG
      k__Bacteria;p__Firmicutes;c__Clostridia;o__Clo...
    

    

      TACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCATGTAGGCGGTTCCCTAAGTCGGTCGTGAAAATGCGGTGCTTAACGCCGTATGGCGATCGAAACTGGGGGACTTGAGTGCAGGAGAGGAAAGGGGAACTCCCAGT
      k__Bacteria;p__Firmicutes;c__Clostridia;o__Clo...
    

    

      TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTAATTAAGTTAGTGGTCAAATCCGGAGGCTTCACTTCCGATCGCCATTAAAACTGATTAGCTAGAGAATGGACGAGGTAGGCGGAATAAGTTAA
      k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o_...
    

    

      TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCTGTGTAAGTCTGAAGTGAAAGCCCGGGGCTCAACCCCGGGACTGCTTTGGAAACTGTATAGCTAGAGTGCTGGAGAGGTAAGTGGAATTCCTAG
      k__Bacteria;p__Firmicutes;c__Clostridia;o__Clo...
    

    

      TACGTAGGGGGCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGTGCGTAGGTGGTATGGCAAGTCAGAAGTGAAAACCCAGGGCTTAACTCTGGGACTGCTTTTGAAACTGTCAGACTAGAGTGTAGGAGAGGTAAGCGGAATTCCTAG
      k__Bacteria;p__Firmicutes;c__Clostridia;o__Clo...
    

  



2129 rows × 1 columns

Reads table (Experiment.data)

This is a numpy 2D array or a scipy.Sparse matrix containing the feature X sample reads.

Rows are samples, columns are features.





In [6]:



    


cfs.data



    


















    
Out[6]:








<87x2129 sparse matrix of type '<class 'numpy.float64'>'
	with 21995 stored elements in Compressed Sparse Row format>

Choosing sparse/dense representation of the data

When loading the data, it is by default loaded as a scipy.Sparse.CSR matrix (which is more memory efficient for sparse data).

We can force Calour to load the data as a dense numpy 2D array using the sparse=False parameter in the read_amplicon() function.

We can also convert between sparse and dense using the sparse attribute of the experiment

Convert to dense





In [7]:



    


cfs.sparse=False
cfs.data



    


















    
Out[7]:








array([[3.17744176e+03, 9.53232528e+02, 7.34643695e+02, ...,
        0.00000000e+00, 0.00000000e+00, 0.00000000e+00],
       [2.59231982e+03, 3.83801502e+00, 3.63055475e+00, ...,
        0.00000000e+00, 0.00000000e+00, 0.00000000e+00],
       [1.12373187e+03, 4.78524699e+02, 0.00000000e+00, ...,
        0.00000000e+00, 0.00000000e+00, 0.00000000e+00],
       ...,
       [3.01104327e+03, 0.00000000e+00, 2.22422402e-01, ...,
        0.00000000e+00, 0.00000000e+00, 0.00000000e+00],
       [3.40518245e+02, 1.77466873e+03, 0.00000000e+00, ...,
        0.00000000e+00, 0.00000000e+00, 0.00000000e+00],
       [5.02440604e+02, 0.00000000e+00, 0.00000000e+00, ...,
        3.39941226e+01, 5.10534442e+00, 1.36972655e+00]])

convert to sparse





In [8]:



    


cfs.sparse=True
cfs.data



    


















    
Out[8]:








<87x2129 sparse matrix of type '<class 'numpy.float64'>'
	with 21995 stored elements in Compressed Sparse Row format>

Getting the data

We can use the Experiment.get_data() function to obtain a copy of the data, either as sparse or dense.

sparse=None means keep the original format





In [9]:



    


dat = cfs.get_data(sparse=None)
dat



    


















    
Out[9]:








<87x2129 sparse matrix of type '<class 'numpy.float64'>'
	with 21995 stored elements in Compressed Sparse Row format>

sparse=True returns a sparse representation of the data (copies if needed)





In [10]:



    


dat = cfs.get_data(sparse=True)
dat



    


















    
Out[10]:








<87x2129 sparse matrix of type '<class 'numpy.float64'>'
	with 21995 stored elements in Compressed Sparse Row format>

sparse=False returns a dense representation of the data (copies if needed)





In [11]:



    


dat = cfs.get_data(sparse=False)
dat



    


















    
Out[11]:








array([[3.17744176e+03, 9.53232528e+02, 7.34643695e+02, ...,
        0.00000000e+00, 0.00000000e+00, 0.00000000e+00],
       [2.59231982e+03, 3.83801502e+00, 3.63055475e+00, ...,
        0.00000000e+00, 0.00000000e+00, 0.00000000e+00],
       [1.12373187e+03, 4.78524699e+02, 0.00000000e+00, ...,
        0.00000000e+00, 0.00000000e+00, 0.00000000e+00],
       ...,
       [3.01104327e+03, 0.00000000e+00, 2.22422402e-01, ...,
        0.00000000e+00, 0.00000000e+00, 0.00000000e+00],
       [3.40518245e+02, 1.77466873e+03, 0.00000000e+00, ...,
        0.00000000e+00, 0.00000000e+00, 0.00000000e+00],
       [5.02440604e+02, 0.00000000e+00, 0.00000000e+00, ...,
        3.39941226e+01, 5.10534442e+00, 1.36972655e+00]])

we can also force copying the data using copy=True





In [12]:



    


dat = cfs.get_data(sparse=None, copy=False)
dat is cfs.data



    


















    
Out[12]:








True

















In [13]:



    


dat = cfs.get_data(sparse=None, copy=True)
dat is cfs.data



    


















    
Out[13]:








False

getting a single entry based on feature and sample values

We can use the __getitem(sampleid, featureid)__ attribute.





In [14]:



    


cfs['ERR1331815','TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGACGCTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGGTGTCTTGAGTACAGTAGAGGCAGGCGGAATTCGTGG']



    


















    
Out[14]:








1407.0828439786792

Saving an Experiment

Save everything (biom table+sample/feature mapping files)

By default saves as an HDF5 biom table. We can save as a text biom table insteadusing fmt="txt" parameter





In [15]:



    


cfs.save('cfs')



    











In [16]:



    


!ls cfs*



    


















    






cfs.biom        cfs_feature.txt cfs_sample.txt

















In [ ]:

Content source: RNAer/Calour

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