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 [ ]: