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Procrustes transformation for comparing 90- vs 150-bp Deblur tables





In [ ]:



    


import pandas as pd
import numpy as np

Note: this notebook requires operating on the original UniFrac distances matrices, which are very large.

To reproduce, download the following files from ftp://ftp.microbio.me/emp/release1/results/beta_diversity/deblur/:

emp_150_gg_1k_unweighted_unifrac.txt
emp_90_gg_1k_unweighted_unifrac.txt




In [34]:



    


# read in samples 

samples_150 = pd.read_csv('./emp_150_gg_1k_unweighted_unifrac.txt', nrows=1, sep ='\t', header=None).T[0][1:]
samples_90 = pd.read_csv('./emp_90_gg_1k_unweighted_unifrac.txt', nrows=1, sep ='\t', header=None).T[0][1:]



    











In [18]:



    


# read in sample map

subset_2k_map = pd.read_csv('../../data/mapping-files/emp_qiime_mapping_subset_2k.tsv', header=0, sep='\t')
subset_2k_map.head()



    


















    
Out[18]:










  
    

      
      #SampleID
      BarcodeSequence
      LinkerPrimerSequence
      Description
      host_subject_id
      study_id
      title
      principal_investigator
      doi
      ebi_accession
      ...
      adiv_shannon
      adiv_faith_pd
      temperature_deg_c
      ph
      salinity_psu
      oxygen_mg_per_l
      phosphate_umol_per_l
      ammonium_umol_per_l
      nitrate_umol_per_l
      sulfate_umol_per_l
    

  
  
    

      0
      550.L1S116.s.1.sequence
      ATGCCTGAGCAG
      GTGCCAGCMGCCGCGGTAA
      sample_20 stool
      F4
      550
      Moving pictures of the human microbiome
      Rob Knight
      10.1186/gb-2011-12-5-r50
      ERP021896
      ...
      3.867414
      12.457989
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      1
      550.L1S119.s.1.sequence
      CAGCACTAAGCG
      GTGCCAGCMGCCGCGGTAA
      sample_23 stool
      F4
      550
      Moving pictures of the human microbiome
      Rob Knight
      10.1186/gb-2011-12-5-r50
      ERP021896
      ...
      3.265164
      10.719448
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      2
      550.L1S164.s.1.sequence
      ATGTACGGCGAC
      GTGCCAGCMGCCGCGGTAA
      sample_73 stool
      M3
      550
      Moving pictures of the human microbiome
      Rob Knight
      10.1186/gb-2011-12-5-r50
      ERP021896
      ...
      3.661124
      14.214158
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      3
      550.L1S194.s.1.sequence
      CGAAGACTGCTG
      GTGCCAGCMGCCGCGGTAA
      sample_105 stool
      M3
      550
      Moving pictures of the human microbiome
      Rob Knight
      10.1186/gb-2011-12-5-r50
      ERP021896
      ...
      4.439943
      12.012602
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      4
      550.L1S20.s.1.sequence
      ACGGTGAGTGTC
      GTGCCAGCMGCCGCGGTAA
      sample_112 stool
      F4
      550
      Moving pictures of the human microbiome
      Rob Knight
      10.1186/gb-2011-12-5-r50
      ERP021896
      ...
      3.327601
      11.758069
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      5
      550.L1S26.s.1.sequence
      ACAGCAGTGGTC
      GTGCCAGCMGCCGCGGTAA
      sample_175 stool
      F4
      550
      Moving pictures of the human microbiome
      Rob Knight
      10.1186/gb-2011-12-5-r50
      ERP021896
      ...
      3.272025
      10.390166
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      6
      550.L1S264.s.1.sequence
      CTGTATCGTATG
      GTGCCAGCMGCCGCGGTAA
      sample_180 stool
      M3
      550
      Moving pictures of the human microbiome
      Rob Knight
      10.1186/gb-2011-12-5-r50
      ERP021896
      ...
      5.732025
      19.540809
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      7
      550.L1S273.s.1.sequence
      CCTAGTACTGAT
      GTGCCAGCMGCCGCGGTAA
      sample_189 stool
      M3
      550
      Moving pictures of the human microbiome
      Rob Knight
      10.1186/gb-2011-12-5-r50
      ERP021896
      ...
      4.191533
      14.265016
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      8
      550.L2S103.s.2.sequence
      AGCACGAGCCTA
      GTGCCAGCMGCCGCGGTAA
      sample_380 sebum
      F4
      550
      Moving pictures of the human microbiome
      Rob Knight
      10.1186/gb-2011-12-5-r50
      ERP021896
      ...
      7.570207
      52.371958
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      9
      550.L2S144.s.2.sequence
      AGTACGCTCGAG
      GTGCCAGCMGCCGCGGTAA
      sample_425 sebum
      F4
      550
      Moving pictures of the human microbiome
      Rob Knight
      10.1186/gb-2011-12-5-r50
      ERP021896
      ...
      6.181649
      38.653723
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      10
      550.L2S164.s.2.sequence
      ACTACAGCCTAT
      GTGCCAGCMGCCGCGGTAA
      sample_447 sebum
      F4
      550
      Moving pictures of the human microbiome
      Rob Knight
      10.1186/gb-2011-12-5-r50
      ERP021896
      ...
      5.828009
      37.769790
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      11
      550.L2S166.s.2.sequence
      AGATCGGCTCGA
      GTGCCAGCMGCCGCGGTAA
      sample_449 sebum
      F4
      550
      Moving pictures of the human microbiome
      Rob Knight
      10.1186/gb-2011-12-5-r50
      ERP021896
      ...
      5.952527
      42.317611
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      12
      550.L2S303.s.2.sequence
      CTCATGTACAGT
      GTGCCAGCMGCCGCGGTAA
      sample_597 sebum
      M3
      550
      Moving pictures of the human microbiome
      Rob Knight
      10.1186/gb-2011-12-5-r50
      ERP021896
      ...
      1.868610
      17.649715
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      13
      550.L2S377.s.2.sequence
      CCTCTCGTGATC
      GTGCCAGCMGCCGCGGTAA
      sample_676 sebum
      M3
      550
      Moving pictures of the human microbiome
      Rob Knight
      10.1186/gb-2011-12-5-r50
      ERP021896
      ...
      6.057640
      35.644789
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      14
      550.L4S1.s.4.sequence
      CATGGCTACACA
      GTGCCAGCMGCCGCGGTAA
      sample_1111 sebum
      M3
      550
      Moving pictures of the human microbiome
      Rob Knight
      10.1186/gb-2011-12-5-r50
      ERP021896
      ...
      4.850969
      34.136518
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      15
      550.L4S102.s.4.sequence
      GCAATAGCTGCT
      GTGCCAGCMGCCGCGGTAA
      sample_1115 sebum
      M3
      550
      Moving pictures of the human microbiome
      Rob Knight
      10.1186/gb-2011-12-5-r50
      ERP021896
      ...
      7.066361
      53.006615
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      16
      550.L4S122.s.4.sequence
      GACCACTACGAT
      GTGCCAGCMGCCGCGGTAA
      sample_1137 sebum
      M3
      550
      Moving pictures of the human microbiome
      Rob Knight
      10.1186/gb-2011-12-5-r50
      ERP021896
      ...
      4.212268
      25.715900
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      17
      550.L4S140.s.4.sequence
      GAGTCTGAGTCT
      GTGCCAGCMGCCGCGGTAA
      sample_1157 sebum
      M3
      550
      Moving pictures of the human microbiome
      Rob Knight
      10.1186/gb-2011-12-5-r50
      ERP021896
      ...
      2.630993
      13.920620
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      18
      550.L4S158.s.4.sequence
      GCAGGATAGATA
      GTGCCAGCMGCCGCGGTAA
      sample_1176 sebum
      M3
      550
      Moving pictures of the human microbiome
      Rob Knight
      10.1186/gb-2011-12-5-r50
      ERP021896
      ...
      5.616810
      30.118912
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      19
      550.L4S161.s.4.sequence
      GAAGTCTCGCAT
      GTGCCAGCMGCCGCGGTAA
      sample_1180 sebum
      M3
      550
      Moving pictures of the human microbiome
      Rob Knight
      10.1186/gb-2011-12-5-r50
      ERP021896
      ...
      7.304861
      55.092754
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      20
      550.L4S183.s.4.sequence
      GCGGATGTGACT
      GTGCCAGCMGCCGCGGTAA
      sample_1204 sebum
      M3
      550
      Moving pictures of the human microbiome
      Rob Knight
      10.1186/gb-2011-12-5-r50
      ERP021896
      ...
      4.891649
      24.036843
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      21
      550.L5S119.s.5.sequence
      CAGCACTAAGCG
      GTGCCAGCMGCCGCGGTAA
      sample_1403 saliva
      F4
      550
      Moving pictures of the human microbiome
      Rob Knight
      10.1186/gb-2011-12-5-r50
      ERP021896
      ...
      3.647179
      9.600555
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      22
      550.L5S224.s.5.sequence
      CTGCAGTACTTA
      GTGCCAGCMGCCGCGGTAA
      sample_1519 saliva
      F4
      550
      Moving pictures of the human microbiome
      Rob Knight
      10.1186/gb-2011-12-5-r50
      ERP021896
      ...
      3.869599
      10.713225
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      23
      550.L5S258.s.5.sequence
      CGAGTCTAGTTG
      GTGCCAGCMGCCGCGGTAA
      sample_1556 saliva
      M3
      550
      Moving pictures of the human microbiome
      Rob Knight
      10.1186/gb-2011-12-5-r50
      ERP021896
      ...
      3.841479
      10.921526
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      24
      550.L6S104.s.6.sequence
      TAGATCCTCGAT
      GTGCCAGCMGCCGCGGTAA
      sample_1653 saliva
      M3
      550
      Moving pictures of the human microbiome
      Rob Knight
      10.1186/gb-2011-12-5-r50
      ERP021896
      ...
      4.329496
      11.399017
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      25
      550.L6S144.s.6.sequence
      TAGCGGATCACG
      GTGCCAGCMGCCGCGGTAA
      sample_1695 saliva
      M3
      550
      Moving pictures of the human microbiome
      Rob Knight
      10.1186/gb-2011-12-5-r50
      ERP021896
      ...
      3.687083
      10.642233
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      26
      550.L6S149.s.6.sequence
      GTGTCTACATTG
      GTGCCAGCMGCCGCGGTAA
      sample_1700 saliva
      M3
      550
      Moving pictures of the human microbiome
      Rob Knight
      10.1186/gb-2011-12-5-r50
      ERP021896
      ...
      4.226336
      12.062299
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      27
      550.L6S176.s.6.sequence
      TAGTCGTCTAGT
      GTGCCAGCMGCCGCGGTAA
      sample_1730 saliva
      M3
      550
      Moving pictures of the human microbiome
      Rob Knight
      10.1186/gb-2011-12-5-r50
      ERP021896
      ...
      3.991563
      11.172998
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      28
      550.L6S186.s.6.sequence
      GTAGCTGACGCA
      GTGCCAGCMGCCGCGGTAA
      sample_1741 saliva
      M3
      550
      Moving pictures of the human microbiome
      Rob Knight
      10.1186/gb-2011-12-5-r50
      ERP021896
      ...
      4.099716
      11.555792
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      29
      550.L6S197.s.6.sequence
      ACTCACGGTATG
      GTGCCAGCMGCCGCGGTAA
      sample_1752 saliva
      M3
      550
      Moving pictures of the human microbiome
      Rob Knight
      10.1186/gb-2011-12-5-r50
      ERP021896
      ...
      3.953951
      10.386101
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

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

    

      1970
      2382.GM.181.R4.leav.10.12.lane8.NoIndex.L008.s...
      CGATGTGTGGTT
      GTGCCAGCMGCCGCGGTAA
      Leaves
      HS4
      2382
      The soil microbiome influences grapevine-assoc...
      Jack Gilbert
      10.1128/mBio.02527-14
      ERP006348
      ...
      1.335486
      7.612504
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      1971
      2382.GM.181.R4.gp.10.12.lane8.NoIndex.L008.seq...
      GATCCTCATGCG
      GTGCCAGCMGCCGCGGTAA
      Grapes
      HS4
      2382
      The soil microbiome influences grapevine-assoc...
      Jack Gilbert
      10.1128/mBio.02527-14
      ERP006348
      ...
      0.316466
      5.129634
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      1972
      2382.GM.181.R3.rhizo.10.12.lane7.NoIndex.L007....
      TATCCAAGCGCA
      GTGCCAGCMGCCGCGGTAA
      Rhizosphere
      HS4
      2382
      The soil microbiome influences grapevine-assoc...
      Jack Gilbert
      10.1128/mBio.02527-14
      ERP006348
      ...
      9.029518
      113.700721
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      1973
      2382.GM.181.R3.leav.10.12.lane8.NoIndex.L008.s...
      TCCATCGACGTG
      GTGCCAGCMGCCGCGGTAA
      Leaves
      HS4
      2382
      The soil microbiome influences grapevine-assoc...
      Jack Gilbert
      10.1128/mBio.02527-14
      ERP006348
      ...
      0.336742
      4.742170
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      1974
      2382.GM.181.R3.gp.10.12.lane8.NoIndex.L008.seq...
      AGACATACCGTA
      GTGCCAGCMGCCGCGGTAA
      Grapes
      HS4
      2382
      The soil microbiome influences grapevine-assoc...
      Jack Gilbert
      10.1128/mBio.02527-14
      ERP006348
      ...
      0.121966
      4.951791
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      1975
      2382.GM.181.R2.root.10.12.lane7.NoIndex.L007.s...
      GGCATGTTATCG
      GTGCCAGCMGCCGCGGTAA
      Roots
      HS4
      2382
      The soil microbiome influences grapevine-assoc...
      Jack Gilbert
      10.1128/mBio.02527-14
      ERP006348
      ...
      6.523943
      48.856413
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      1976
      2382.GM.181.R2.rhizo.10.12.lane7.NoIndex.L007....
      ACCAATCTCGGC
      GTGCCAGCMGCCGCGGTAA
      Rhizosphere
      HS4
      2382
      The soil microbiome influences grapevine-assoc...
      Jack Gilbert
      10.1128/mBio.02527-14
      ERP006348
      ...
      8.553171
      98.373702
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      1977
      2382.GM.181.R2.leav.10.12.lane8.NoIndex.L008.s...
      AGCTCTAGAAAC
      GTGCCAGCMGCCGCGGTAA
      Leaves
      HS4
      2382
      The soil microbiome influences grapevine-assoc...
      Jack Gilbert
      10.1128/mBio.02527-14
      ERP006348
      ...
      0.031598
      4.116123
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      1978
      2382.GM.181.R2.gp.10.12.lane8.NoIndex.L008.seq...
      GATCATTCTCTC
      GTGCCAGCMGCCGCGGTAA
      Grapes
      HS4
      2382
      The soil microbiome influences grapevine-assoc...
      Jack Gilbert
      10.1128/mBio.02527-14
      ERP006348
      ...
      0.144597
      4.259524
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      1979
      2382.GM.181.R1.leav.10.12.lane8.NoIndex.L008.s...
      CCAGACCGCTAT
      GTGCCAGCMGCCGCGGTAA
      Leaves
      HS4
      2382
      The soil microbiome influences grapevine-assoc...
      Jack Gilbert
      10.1128/mBio.02527-14
      ERP006348
      ...
      1.098354
      8.048152
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      1980
      2382.GM.181.R1.gp.10.12.lane8.NoIndex.L008.seq...
      TCTGAGGTTGCC
      GTGCCAGCMGCCGCGGTAA
      Grapes
      HS4
      2382
      The soil microbiome influences grapevine-assoc...
      Jack Gilbert
      10.1128/mBio.02527-14
      ERP006348
      ...
      0.049765
      4.818847
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      1981
      2382.DPOO1.C1.HA.5.650.gp.9.12.lane8.NoIndex.L...
      ACCTTACACCTT
      GTGCCAGCMGCCGCGGTAA
      Grapes
      HS3
      2382
      The soil microbiome influences grapevine-assoc...
      Jack Gilbert
      10.1128/mBio.02527-14
      ERP006348
      ...
      0.172636
      4.406474
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      1982
      2382.DPOO1.C1.HA.5.649.leav.9.12.lane8.NoIndex...
      AACCATGCCAAC
      GTGCCAGCMGCCGCGGTAA
      Leaves
      HS7
      2382
      The soil microbiome influences grapevine-assoc...
      Jack Gilbert
      10.1128/mBio.02527-14
      ERP006348
      ...
      0.020367
      3.148375
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      1983
      2382.DPOO1.C1.HA.5.648.root.9.12.lane7.NoIndex...
      GAGGTTCTTGAC
      GTGCCAGCMGCCGCGGTAA
      Roots
      HS7
      2382
      The soil microbiome influences grapevine-assoc...
      Jack Gilbert
      10.1128/mBio.02527-14
      ERP006348
      ...
      6.035013
      54.134147
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      1984
      2382.DPOO1.C1.HA.5.448.root.4.12.lane7.NoIndex...
      AGCCTCATGATG
      GTGCCAGCMGCCGCGGTAA
      Roots
      HS10
      2382
      The soil microbiome influences grapevine-assoc...
      Jack Gilbert
      10.1128/mBio.02527-14
      ERP006348
      ...
      6.658723
      61.613640
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      1985
      2382.DPOO1.C1.HA.4.645.gp.9.12.lane8.NoIndex.L...
      ACTAGCGTTCAG
      GTGCCAGCMGCCGCGGTAA
      Grapes
      HS7
      2382
      The soil microbiome influences grapevine-assoc...
      Jack Gilbert
      10.1128/mBio.02527-14
      ERP006348
      ...
      0.047735
      2.771104
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      1986
      2382.DPOO1.C1.HA.4.644.leav.9.12.lane8.NoIndex...
      GGTAAGTTTGAC
      GTGCCAGCMGCCGCGGTAA
      Leaves
      HS7
      2382
      The soil microbiome influences grapevine-assoc...
      Jack Gilbert
      10.1128/mBio.02527-14
      ERP006348
      ...
      0.018037
      1.768118
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      1987
      2382.DPOO1.C1.HA.3.640.gp.9.12.lane8.NoIndex.L...
      CCGAAGATTCTG
      GTGCCAGCMGCCGCGGTAA
      Grapes
      HS7
      2382
      The soil microbiome influences grapevine-assoc...
      Jack Gilbert
      10.1128/mBio.02527-14
      ERP006348
      ...
      0.096775
      4.252410
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      1988
      2382.DPOO1.C1.HA.3.639.leav.9.12.lane8.NoIndex...
      TGGAATTCGGCT
      GTGCCAGCMGCCGCGGTAA
      Leaves
      HS7
      2382
      The soil microbiome influences grapevine-assoc...
      Jack Gilbert
      10.1128/mBio.02527-14
      ERP006348
      ...
      0.047049
      3.368435
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      1989
      2382.DPOO1.C1.HA.3.32.r1.leav.6.11.lane8.NoInd...
      TGTATCTTCACC
      GTGCCAGCMGCCGCGGTAA
      Leaves
      HS9
      2382
      The soil microbiome influences grapevine-assoc...
      Jack Gilbert
      10.1128/mBio.02527-14
      ERP006348
      ...
      0.040234
      5.070915
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      1990
      2382.DPOO1.C1.HA.3.238.root.9.11.lane1.NoIndex...
      ATCGTGTGTTGG
      GTGCCAGCMGCCGCGGTAA
      Roots
      HS10
      2382
      The soil microbiome influences grapevine-assoc...
      Jack Gilbert
      10.1128/mBio.02527-14
      ERP006348
      ...
      7.417508
      76.719597
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      1991
      2382.DPOO1.C1.HA.2.635.gp.9.12.lane8.NoIndex.L...
      GGCGTTGCATTC
      GTGCCAGCMGCCGCGGTAA
      Grapes
      HS7
      2382
      The soil microbiome influences grapevine-assoc...
      Jack Gilbert
      10.1128/mBio.02527-14
      ERP006348
      ...
      0.015675
      2.704737
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      1992
      2382.DPOO1.C1.HA.2.634.leav.9.12.lane8.NoIndex...
      TCTTCAACTACC
      GTGCCAGCMGCCGCGGTAA
      Leaves
      HS7
      2382
      The soil microbiome influences grapevine-assoc...
      Jack Gilbert
      10.1128/mBio.02527-14
      ERP006348
      ...
      0.088071
      2.056739
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      1993
      2382.DPOO1.C1.HA.2.633.root.9.12.lane7.NoIndex...
      ATGTCACCGCTG
      GTGCCAGCMGCCGCGGTAA
      Roots
      HS1
      2382
      The soil microbiome influences grapevine-assoc...
      Jack Gilbert
      10.1128/mBio.02527-14
      ERP006348
      ...
      7.351779
      75.716918
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      1994
      2382.DPOO1.C1.HA.2.433.root.4.12.lane7.NoIndex...
      CCAAACTCGTCG
      GTGCCAGCMGCCGCGGTAA
      Roots
      HS10
      2382
      The soil microbiome influences grapevine-assoc...
      Jack Gilbert
      10.1128/mBio.02527-14
      ERP006348
      ...
      7.070601
      69.265327
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      1995
      2382.DPOO1.C1.HA.1.630.gp.9.12.lane8.NoIndex.L...
      TTGCGACAAAGT
      GTGCCAGCMGCCGCGGTAA
      Grapes
      HS7
      2382
      The soil microbiome influences grapevine-assoc...
      Jack Gilbert
      10.1128/mBio.02527-14
      ERP006348
      ...
      0.092204
      3.604761
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      1996
      2382.DPOO1.C1.HA.1.629.leav.9.12.lane8.NoIndex...
      ACTACCTCTTCA
      GTGCCAGCMGCCGCGGTAA
      Leaves
      HS7
      2382
      The soil microbiome influences grapevine-assoc...
      Jack Gilbert
      10.1128/mBio.02527-14
      ERP006348
      ...
      0.168218
      2.056739
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      1997
      2382.DPOO1.C1.HA.1.628.root.9.12.lane7.NoIndex...
      AGATGTCCGTCA
      GTGCCAGCMGCCGCGGTAA
      Roots
      HS7
      2382
      The soil microbiome influences grapevine-assoc...
      Jack Gilbert
      10.1128/mBio.02527-14
      ERP006348
      ...
      6.728780
      70.312703
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      1998
      2382.DPOO1.C1.HA.1.428.root.4.12.lane7.NoIndex...
      ATGTTTAGACGG
      GTGCCAGCMGCCGCGGTAA
      Roots
      HS10
      2382
      The soil microbiome influences grapevine-assoc...
      Jack Gilbert
      10.1128/mBio.02527-14
      ERP006348
      ...
      6.353810
      50.767095
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

    

      1999
      2382.DPOO1.C1.HA.1.228.root.9.11.lane1.NoIndex...
      TAGTGCATTCGG
      GTGCCAGCMGCCGCGGTAA
      Roots
      HS10
      2382
      The soil microbiome influences grapevine-assoc...
      Jack Gilbert
      10.1128/mBio.02527-14
      ERP006348
      ...
      7.228462
      83.205352
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
      Not applicable
    

  



2000 rows × 76 columns



















In [45]:



    


# reduce map

subset_2k_map_90_100 = subset_2k_map.loc[(subset_2k_map['#SampleID'].isin(samples_150)) &
                                         (subset_2k_map['#SampleID'].isin(samples_90)),]



    











In [46]:



    


# pick N random sequences and write to file

subset_2k_map_90_100.sample(n=200)['#SampleID'].to_csv('./200_samples.txt', index=False)



    











In [47]:



    


# filter distance matrices by 

!filter_distance_matrix.py -i ./emp_150_gg_1k_unweighted_unifrac.txt \
-o ./emp_150_gg_1k_unweighted_unifrac.200.txt \
--sample_id_fp ./200_samples.txt

!filter_distance_matrix.py -i ./emp_90_gg_1k_unweighted_unifrac.txt \
-o ./emp_90_gg_1k_unweighted_unifrac.200.txt \
--sample_id_fp ./200_samples.txt



    











In [48]:



    


# compute PC

!principal_coordinates.py -i ./emp_150_gg_1k_unweighted_unifrac.200.txt -o ./emp_150_gg_1k_unweighted_unifrac.200.txt.pc
!principal_coordinates.py -i ./emp_90_gg_1k_unweighted_unifrac.200.txt -o ./emp_90_gg_1k_unweighted_unifrac.200.txt.pc



    


















    






/home/jgsanders/miniconda/envs/qiime/lib/python2.7/site-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:107: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.0380954766005 and the largest is 9.52380296681.
  RuntimeWarning
/home/jgsanders/miniconda/envs/qiime/lib/python2.7/site-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:107: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.0348895730356 and the largest is 9.35412012146.
  RuntimeWarning

















In [50]:



    


# compute procrustes

!transform_coordinate_matrices.py -i emp_90_gg_1k_unweighted_unifrac.200.txt.pc,emp_150_gg_1k_unweighted_unifrac.200.txt.pc  \
-r 999 \
-o procrustes_results/



    











In [51]:



    


# make emperor plot of procrustes

!make_emperor.py -c -i procrustes_results/ \
-o procrustes_results/plots/ \
-m ./emp_qiime_mapping_subset_2k_20170606.tsv

Content source: cuttlefishh/emp

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