Learn about how calour stores the data of an experiment
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
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
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 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
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
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
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>
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
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]])
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>
We can use the Experiment.get_data() function to obtain a copy of
the data, either as sparse or dense.
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>
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>
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]])
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
We can use the _getitem(sampleid, featureid)_ attribute.
In [14]:
cfs['ERR1331815','TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGACGCTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGGTGTCTTGAGTACAGTAGAGGCAGGCGGAATTCGTGG']
Out[14]:
1407.0828439786792