[1] "-----------> docopt settings---------------------"
[1] "Usage: DiversityPlots_v1.R [options]\n  --help            show this screen.\n  --wdir PATH       give path to working dir /project main dir  [default: pwd ].\n  --indir PATH      give path to input files directory [default: profiles/merged_tables ].\n  --mfile NAME      give name of mapping file [default: mapping.txt ].\n  --outdir NAME     give path & name of output directory to create [default: pwd/profiles/DiversityPlots]."
List of 10
 $ --help  : logi FALSE
 $ --wdir  : chr "/outputs/tmp"
 $ --indir : chr "/outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/"
 $ --mfile : chr "/outputs/TAXprofiles/readsTAX_plusPFV/DivPlots/tmp_mapping_file.txt"
 $ --outdir: chr "/outputs/TAXprofiles/readsTAX_plusPFV/DivPlots/"
 $ help    : logi FALSE
 $ wdir    : chr "/outputs/tmp"
 $ indir   : chr "/outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/"
 $ mfile   : chr "/outputs/TAXprofiles/readsTAX_plusPFV/DivPlots/tmp_mapping_file.txt"
 $ outdir  : chr "/outputs/TAXprofiles/readsTAX_plusPFV/DivPlots/"
NULL
[1] "-----------> docopt settings------^^^^-----------"
               SampleID Description TreatmentGroup
SRR12904817 SRR12904817 SRR12904817       12 month
SRR12904818 SRR12904818 SRR12904818       12 month
SRR12904821 SRR12904821 SRR12904821        1 month
                                ForwardFastqFile
SRR12904817 /inputs/SRR12904817_1_2Msub.fastq.gz
SRR12904818 /inputs/SRR12904818_1_2Msub.fastq.gz
SRR12904821 /inputs/SRR12904821_1_2Msub.fastq.gz
                                ReverseFastqFile
SRR12904817 /inputs/SRR12904817_2_2Msub.fastq.gz
SRR12904818 /inputs/SRR12904818_2_2Msub.fastq.gz
SRR12904821 /inputs/SRR12904821_2_2Msub.fastq.gz
[1] "-----------> read in mapping file^^^"
          SRR12904817 SRR12904818 SRR12904821
id204434            0           0           1
id2789425           0           0           1
id1659              0           0           1
id461393            0           0           1
id1655             14           0           1
id706438            0           2           0
[1] "-----------> read in Counts^^^"
           Kingdom          Phylum         Class           Order
id204434  Bacteria Acidobacteriota   Terriglobia   Terriglobales
id2789425 Bacteria  Actinomycetota Actinomycetes Actinomycetales
id1659    Bacteria  Actinomycetota Actinomycetes Actinomycetales
id461393  Bacteria  Actinomycetota Actinomycetes Actinomycetales
id1655    Bacteria  Actinomycetota Actinomycetes Actinomycetales
id706438  Bacteria  Actinomycetota Actinomycetes Actinomycetales
                     Family       Genus                    Species
id204434  Acidobacteriaceae                   Acidobacteriaceae_sp
id2789425  Actinomycetaceae Actinomyces        Actinomyces_HMT_175
id1659     Actinomycetaceae Actinomyces       Actinomyces_israelii
id461393   Actinomycetaceae Actinomyces   Actinomyces_massiliensis
id1655     Actinomycetaceae Actinomyces     Actinomyces_naeslundii
id706438   Actinomycetaceae Actinomyces Actinomyces_oral_taxon_171
[1] "-----------> read in TAX^^^"
[1] "-----------> Calculating alpha diversity indexes"
            SpRichness  Evenness NumbReads  Shannon InvSimpson    chao1
SRR12904817        306 0.4316647     57109 2.470670   7.390371 578.5806
SRR12904818        285 0.3124265    187422 1.765987   3.824121 506.8333
SRR12904821        301 0.2816983     98493 1.607683   3.586761 626.7286
[1] "-----------> Adding these apha indices to metadata ^^^"
         group1   group2   variable  value
         <char>   <char>     <fctr>  <num>
 1: SRR12904817 12 month SpRichness 306.00
 2: SRR12904818 12 month SpRichness 285.00
 3: SRR12904821  1 month SpRichness 301.00
 4: SRR12904817 12 month   Evenness   0.43
 5: SRR12904818 12 month   Evenness   0.31
 6: SRR12904821  1 month   Evenness   0.28
 7: SRR12904817 12 month    Shannon   2.47
 8: SRR12904818 12 month    Shannon   1.77
 9: SRR12904821  1 month    Shannon   1.61
10: SRR12904817 12 month InvSimpson   7.39
11: SRR12904818 12 month InvSimpson   3.82
12: SRR12904821  1 month InvSimpson   3.59
[1] "-----------> plotting alpha diversity"
null device 
          1 
[1] "-----------> prepping AMPVIS2 object"
[1] "-----------> checking some AMPVIS2 data"
          SRR12904817 SRR12904818 SRR12904821
id204434            0           0           1
id2789425           0           0           1
id1659              0           0           1
id461393            0           0           1
id1655             14           0           1
id706438            0           2           0
           Kingdom          Phylum         Class           Order
id204434  Bacteria Acidobacteriota   Terriglobia   Terriglobales
id2789425 Bacteria  Actinomycetota Actinomycetes Actinomycetales
id1659    Bacteria  Actinomycetota Actinomycetes Actinomycetales
id461393  Bacteria  Actinomycetota Actinomycetes Actinomycetales
                     Family       Genus                  Species       OTU
id204434  Acidobacteriaceae                 Acidobacteriaceae_sp  id204434
id2789425  Actinomycetaceae Actinomyces      Actinomyces_HMT_175 id2789425
id1659     Actinomycetaceae Actinomyces     Actinomyces_israelii    id1659
id461393   Actinomycetaceae Actinomyces Actinomyces_massiliensis  id461393
               SampleID Description TreatmentGroup
SRR12904817 SRR12904817 SRR12904817       12 month
SRR12904818 SRR12904818 SRR12904818       12 month
SRR12904821 SRR12904821 SRR12904821        1 month
                                ForwardFastqFile
SRR12904817 /inputs/SRR12904817_1_2Msub.fastq.gz
SRR12904818 /inputs/SRR12904818_1_2Msub.fastq.gz
SRR12904821 /inputs/SRR12904821_1_2Msub.fastq.gz
                                ReverseFastqFile SpRichness Evenness NumbReads
SRR12904817 /inputs/SRR12904817_2_2Msub.fastq.gz        306     0.43     57109
SRR12904818 /inputs/SRR12904818_2_2Msub.fastq.gz        285     0.31    187422
SRR12904821 /inputs/SRR12904821_2_2Msub.fastq.gz        301     0.28     98493
            Shannon InvSimpson  chao1
SRR12904817    2.47       7.39 578.58
SRR12904818    1.77       3.82 506.83
SRR12904821    1.61       3.59 626.73
[1] "-----------> checking AMPVIS2 data ^^^"
[1] "-----------> making PCOA plot"
null device 
          1 
[1] "-----------> making nMDS plot"
null device 
          1 
[1] "-----------> making heatmap profile graph"
null device 
          1 
[1] "-----------> making rarecurve graph"
null device 
          1 
[1] "-----------> making rank abundance / Whittaker plot"
null device 
          1 
