Description

The relatively abundant taxa seem to be present in all gradient fractions.
- >0.1% pre-fractionation abundance (at least for 1 12C-con gradient)
Goal:
- For all 12C-Con gradients determine the detection threshold:
  - What is the % abundance cutoff where taxa are no longer detected in all gradients

Setting parameters



In [2]:

    
%load_ext rpy2.ipython



In [8]:

    
%%R
physeqDir = '/var/seq_data/fullCyc/MiSeq_16SrRNA/515f-806r/lib1-7/phyloseq/'
physeq_bulk_core = 'bulk-core'
physeq_SIP_core = 'SIP-core_unk'

Init



In [4]:

    
%%R
library(dplyr)
library(tidyr)
library(ggplot2)
library(phyloseq)









    



/opt/anaconda/lib/python2.7/site-packages/rpy2/robjects/functions.py:106: UserWarning: 
Attaching package: ‘dplyr’


  res = super(Function, self).__call__(*new_args, **new_kwargs)
/opt/anaconda/lib/python2.7/site-packages/rpy2/robjects/functions.py:106: UserWarning: The following objects are masked from ‘package:stats’:

    filter, lag


  res = super(Function, self).__call__(*new_args, **new_kwargs)
/opt/anaconda/lib/python2.7/site-packages/rpy2/robjects/functions.py:106: UserWarning: The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union


  res = super(Function, self).__call__(*new_args, **new_kwargs)

Mapping bulk and SIP data

SIP dataset



In [9]:

    
%%R
F = file.path(physeqDir, physeq_SIP_core)
physeq.SIP = readRDS(F)
physeq.SIP.m = physeq.SIP %>% sample_data
physeq.SIP









    





phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 12358 taxa and 963 samples ]
sample_data() Sample Data:       [ 963 samples by 17 sample variables ]
tax_table()   Taxonomy Table:    [ 12358 taxa by 8 taxonomic ranks ]
phy_tree()    Phylogenetic Tree: [ 12358 tips and 12357 internal nodes ]

Pre-fraction dataset



In [5]:

    
%%R
F = file.path(physeqDir, physeq_bulk_core)
physeq.bulk = readRDS(F)
physeq.bulk.m = physeq.bulk %>% sample_data
physeq.bulk









    





phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 4950 taxa and 9 samples ]
sample_data() Sample Data:       [ 9 samples by 17 sample variables ]
tax_table()   Taxonomy Table:    [ 4950 taxa by 8 taxonomic ranks ]
phy_tree()    Phylogenetic Tree: [ 4950 tips and 4949 internal nodes ]



In [7]:

    
%%R 
# parsing out to just 12C-Con gradients
physeq.bulk.f = prune_samples((physeq.bulk.m$Exp_type == 'microcosm_bulk') | 
                         (physeq.bulk.m$Exp_type == 'SIP' & 
                          physeq.bulk.m$Substrate == '12C-Con'),
                         physeq) %>% 
    filter_taxa(function(x) sum(x) > 0, TRUE)
physeq.bulk.f.m = physeq.bulk.f %>% sample_data %>% as.matrix %>% as.data.frame 
physeq.bulk.f









    





phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 4950 taxa and 9 samples ]
sample_data() Sample Data:       [ 9 samples by 17 sample variables ]
tax_table()   Taxonomy Table:    [ 4950 taxa by 8 taxonomic ranks ]
phy_tree()    Phylogenetic Tree: [ 4950 tips and 4949 internal nodes ]



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