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Running SIPSim pipeline to simulate priming_exp gradient dataset

  • Basing simulation params off of priming_exp dataset
    • Including more diffusion (smaller fragment lengths) to see if

Setting variables





In [13]:



    


workDir = '/home/nick/notebook/SIPSim/dev/priming_exp/validation_sample/X12C.700.14.05_moreDif/'
genomeDir = '/home/nick/notebook/SIPSim/dev/priming_exp/genomes/'
otuTableFile = '/var/seq_data/priming_exp/data/otu_table.txt'
metaDataFile = '/var/seq_data/priming_exp/data/allsample_metadata_nomock.txt'
primerFile = '/home/nick/notebook/SIPSim/dev/515F-806R.fna'

cdhit_dir = '/home/nick/notebook/SIPSim/dev/priming_exp/CD-HIT/'
R_dir = '/home/nick/notebook/SIPSim/lib/R/'
figureDir = '/home/nick/notebook/SIPSim/figures/'

# total dataset files
#allAmpFrags = '/home/nick/notebook/SIPSim/dev/bac_genome1210/validation/ampFrags.pkl'
genomeAllDir = '/home/nick/notebook/SIPSim/dev/bac_genome1210/genomes/'
genomeAllIndex = '/home/nick/notebook/SIPSim/dev/bac_genome1210/genomes/genome_index.txt'

# simulation params
comm_richness = 2170
seq_per_fraction = ['lognormal', 10.096, 1.116]

# for making genome_map file for genome fragment simulation
taxonMapFile = os.path.join(cdhit_dir, 'target_taxa.txt')
genomeFilterFile = os.path.join(cdhit_dir, 'genomeFile_seqID_filt.txt')
abundFile = os.path.join(workDir, 'X12C.700.14.05.NA_OTU.txt')

# misc
nprocs = 20

Init





In [14]:



    


import glob
import cPickle as pickle
import copy
from IPython.display import Image



    











In [15]:



    


%load_ext rpy2.ipython



    











In [16]:



    


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



    


















    






/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)
/opt/anaconda/lib/python2.7/site-packages/rpy2/robjects/functions.py:106: UserWarning: Loading required package: grid

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

















In [17]:



    


if not os.path.isdir(workDir):
    os.makedirs(workDir)

Creating a community file from OTU table





In [39]:



    


%%R -i otuTableFile 

tbl.otu = read.delim(otuTableFile, sep='\t')
tbl.otu[1:3,1:5]



    


















    








     OTUId X12C.700.45.01.24 X12C.700.14.06.14 X12C.100.14.05.18
1 OTU.4776               157                34                13
2 OTU.2864                 0                 1                 2
3 OTU.8170                 0                 0                 0
  X12C.700.14.06.05
1               142
2                16
3                 0


















In [40]:



    


%%R
tbl.otu.w = tbl.otu %>%
    gather('sample', 'count', 2:ncol(tbl.otu)) %>%
    group_by(sample) %>%
    mutate(rel_abund_perc = count / sum(count) * 100) %>%
    ungroup %>%
    filter(count > 0, sample == 'X12C.700.14.05.NA') %>%
    mutate(library = '1', rank = row_number(-rel_abund_perc)) %>%
    select(library, 'taxon_name' = OTUId, rel_abund_perc, rank) %>%
    arrange(rank)
tbl.otu.w %>% head(n=5)



    


















    








Source: local data frame [5 x 4]

  library taxon_name rel_abund_perc rank
1       1     OTU.22       2.431002    1
2       1      OTU.1       2.202202    2
3       1     OTU.20       1.892369    3
4       1      OTU.2       1.682635    4
5       1    OTU.108       1.577768    5


















In [41]:



    


%%R -i comm_richness
# number of OTUs
n.OTUs = tbl.otu.w$taxon_name %>% unique %>% length
cat('Number of OTUs:', n.OTUs, '\n')

# assertion
cat('Community richness = number of OTUs?', comm_richness == n.OTUs, '\n')



    


















    








Number of OTUs: 2170 
Community richness = number of OTUs? TRUE 


















In [42]:



    


%%R -i workDir

commFile = paste(c(workDir, 'comm.txt'), collapse='/')
write.table(tbl.otu.w, commFile, sep='\t', quote=F, row.names=F)

Plotting community distribution





In [43]:



    


%%R -i workDir

commFile = paste(c(workDir, 'comm.txt'), collapse='/')
comm = read.delim(commFile, sep='\t')
comm %>% head



    


















    








  library taxon_name rel_abund_perc rank
1       1     OTU.22       2.431002    1
2       1      OTU.1       2.202202    2
3       1     OTU.20       1.892369    3
4       1      OTU.2       1.682635    4
5       1    OTU.108       1.577768    5
6       1      OTU.8       1.201201    6


















In [44]:



    


%%R -w 900 -h 350

ggplot(comm, aes(rank, rel_abund_perc)) +
    geom_point() +
    labs(x='Rank', y='% relative abundance', title='Priming experiment community abundance distribution') +
    theme_bw() +
    theme(
        text = element_text(size=16)
        )

Simulating fragments

Making a genome index file to map genome fasta files to OTUs

  • Will be used for community simulation
  • Just OTUs with association to genomes




In [45]:



    


%%R -i taxonMapFile -i genomeFilterFile 

taxonMap = read.delim(taxonMapFile, sep='\t') %>%
    select(target_genome, OTU) %>%
    distinct()
taxonMap %>% nrow %>% print
taxonMap %>% head(n=3) %>% print

cat('----------------\n')

genomeFilter = read.delim(genomeFilterFile, sep='\t', header=F) 
genomeFilter %>% nrow %>% print
genomeFilter %>% head(n=3) %>% print

cat('----------------\n')

comm = read.delim(commFile, sep='\t') 
comm %>% nrow %>% print
comm %>% head(n=3) %>% print



    


















    








[1] 236
                               target_genome      OTU
1 CP001738_Thermomonospora_curvata_DSM_43183 OTU.8540
2 CP001738_Thermomonospora_curvata_DSM_43183 OTU.9267
3 CP001738_Thermomonospora_curvata_DSM_43183 OTU.1457
----------------
[1] 187
                                                         V1
1                  CP003093_Pseudoxanthomonas_spadix_BD_a59
2                  CP000511_Mycobacterium_vanbaalenii_PYR_1
3 CP003344_Desulfitobacterium_dichloroeliminans_LMG_P_21439
                                                                                                            V2
1                  /home/nick/notebook/SIPSim/dev/bac_genome1210/genomes/Pseudoxanthomonas_spadix_BD-a59.fasta
2                  /home/nick/notebook/SIPSim/dev/bac_genome1210/genomes/Mycobacterium_vanbaalenii_PYR-1.fasta
3 /home/nick/notebook/SIPSim/dev/bac_genome1210/genomes/Desulfitobacterium_dichloroeliminans_LMG_P-21439.fasta
----------------
[1] 2170
  library taxon_name rel_abund_perc rank
1       1     OTU.22       2.431002    1
2       1      OTU.1       2.202202    2
3       1     OTU.20       1.892369    3


















In [46]:



    


%%R
taxonMap$OTU %>% table %>% sort(decreasing=T) %>% head



    


















    








.
    OTU.1    OTU.10   OTU.101   OTU.102 OTU.10237  OTU.1035 
        1         1         1         1         1         1 


















In [47]:



    


%%R

tbl.j = inner_join(taxonMap, genomeFilter, c('target_genome' = 'V1')) %>%
     rename('fasta_file' = V2) %>%
     select(OTU, fasta_file, target_genome)

tbl.j %>% head(n=3)



    


















    








       OTU
1 OTU.8540
2 OTU.9267
3 OTU.1457
                                                                                     fasta_file
1 /home/nick/notebook/SIPSim/dev/bac_genome1210/genomes/Thermomonospora_curvata_DSM_43183.fasta
2 /home/nick/notebook/SIPSim/dev/bac_genome1210/genomes/Thermomonospora_curvata_DSM_43183.fasta
3 /home/nick/notebook/SIPSim/dev/bac_genome1210/genomes/Thermomonospora_curvata_DSM_43183.fasta
                               target_genome
1 CP001738_Thermomonospora_curvata_DSM_43183
2 CP001738_Thermomonospora_curvata_DSM_43183
3 CP001738_Thermomonospora_curvata_DSM_43183


















In [48]:



    


%%R
tbl.j$OTU %>% table %>% sort(decreasing=T) %>% head



    


















    








.
    OTU.1    OTU.10   OTU.101   OTU.102 OTU.10237  OTU.1035 
        1         1         1         1         1         1 


















In [49]:



    


%%R
tbl.j2 = inner_join(tbl.j, comm, c('OTU' = 'taxon_name')) 

n.target.genomes = tbl.j2$OTU %>% unique %>% length
cat('Number of target OTUs: ', n.target.genomes, '\n')
cat('--------\n')
tbl.j2 %>% head(n=3)



    


















    








Number of target OTUs:  108 
--------
       OTU
1 OTU.1457
2   OTU.77
3 OTU.2347
                                                                                        fasta_file
1    /home/nick/notebook/SIPSim/dev/bac_genome1210/genomes/Thermomonospora_curvata_DSM_43183.fasta
2      /home/nick/notebook/SIPSim/dev/bac_genome1210/genomes/Pseudoxanthomonas_spadix_BD-a59.fasta
3 /home/nick/notebook/SIPSim/dev/bac_genome1210/genomes/Micromonospora_aurantiaca_ATCC_27029.fasta
                                  target_genome library rel_abund_perc rank
1    CP001738_Thermomonospora_curvata_DSM_43183       1    0.009533343 1038
2      CP003093_Pseudoxanthomonas_spadix_BD_a59       1    0.019066686  700
3 CP002162_Micromonospora_aurantiaca_ATCC_27029       1    0.004766671 1380


















In [50]:



    


%%R -i workDir

outFile = paste(c(workDir, 'target_genome_index.txt'), collapse='/')
write.table(tbl.j2, outFile, sep='\t', quote=F, row.names=F, col.names=F)

Plotting community abundance distribution of target genomes





In [51]:



    


%%R -w 900 -h 350

ggplot(tbl.j2, aes(rank, rel_abund_perc)) +
    geom_point(size=3, shape='O', color='red') +
    labs(x='Rank', y='% relative abundance', title='Priming experiment community abundance distribution') +
    theme_bw() +
    theme(
        text = element_text(size=16)
        )

Simulating fragments of genomes that match priming_exp bulk OTUs





In [53]:



    


!cd $workDir; \
    SIPSim fragments \
    target_genome_index.txt \
    --fp $genomeDir \
    --fr $primerFile \
    --fld skewed-normal,5000,2000,-5 \
    --flr None,None \
    --nf 10000 \
    --tbl \
    --np $nprocs \
    2> ampFrags.log \
    > ampFrags.txt

Plotting fragment length distribution





In [75]:



    


%%R -i workDir

inFile = paste(c(workDir, 'ampFrags.txt'), collapse='/')

tbl = read.delim(inFile, sep='\t')
tbl %>% head(n=3)



    


















    








  taxon_name                                 scaffoldID fragStart fragLength
1   OTU.1457 CP001738_Thermomonospora_curvata_DSM_43183   2631663       3197
2   OTU.1457 CP001738_Thermomonospora_curvata_DSM_43183   3208231       4687
3   OTU.1457 CP001738_Thermomonospora_curvata_DSM_43183   3872268       4235
    fragGC
1 73.78793
2 70.51419
3 74.30933


















In [76]:



    


%%R -w 950 -h 450

some.taxa = tbl$taxon_name %>% unique %>% head(n=10)

tbl.f = tbl %>% 
    filter(taxon_name %in% some.taxa)

ggplot(tbl.f, aes(fragGC, fragLength)) +
    stat_density2d() +
    labs(x='Fragment G+C', y='Fragment length (bp)') +
    facet_wrap(~ taxon_name, ncol=5) +
    theme_bw() +
    theme(
        text=element_text(size=16),
        axis.title.y=element_text(vjust=1)
        )



    


















    
























In [77]:



    


# re-running simulation with pickled file

!cd $workDir; \
    SIPSim fragments \
    target_genome_index.txt \
    --fp $genomeDir \
    --fr $primerFile \
    --fld skewed-normal,5000,2000,-5 \
    --flr None,None \
    --nf 10000 \
    --np $nprocs \
    2> ampFrags.log \
    > ampFrags.pkl

Simulating fragments of total dataset with a greater diffusion





In [241]:



    


!cd $workDir; \
    SIPSim fragments \
    $genomeAllIndex \
    --fp $genomeAllDir \
    --fr $primerFile \
    --fld skewed-normal,5000,2000,-5 \
    --flr None,None \
    --nf 10000 \
    --np $nprocs \
    2> ampFragsAll.log \
    > ampFragsAll.pkl



    











In [263]:



    


ampFragsAllFile = os.path.join(workDir, 'ampFragsAll.pkl')

Appending fragments from randomly selected genomes of total dataset (n=1210)

  • This is to obtain the richness of the bulk soil community
  • Random OTUs will be named after non-target OTUs

Making list of non-target OTUs





In [242]:



    


%%R -i workDir
# loading files

## target genome index (just OTUs with associated genome)
inFile = paste(c(workDir, 'target_genome_index.txt'), collapse='/')
tbl.target = read.delim(inFile, sep='\t', header=F)
colnames(tbl.target) = c('OTUId', 'fasta_file', 'genome_name')

## comm file of total community OTUs 
commFile = paste(c(workDir, 'comm.txt'), collapse='/')
tbl.comm = read.delim(commFile, sep='\t')



    











In [243]:



    


%%R
# just OTUs w/out an associated genome
tbl.j = anti_join(tbl.comm, tbl.target, c('taxon_name' = 'OTUId'))
n.nontarget.genomes = tbl.j$taxon_name %>% length
cat('Number of non-target genomes: ', n.nontarget.genomes, '\n')
cat('---------\n')
tbl.j %>% head(n=5)



    


















    








Number of non-target genomes:  2062 
---------
  library taxon_name rel_abund_perc rank
1       1  OTU.11779    0.004766671 2170
2       1   OTU.9498    0.004766671 2169
3       1   OTU.3673    0.004766671 2168
4       1    OTU.493    0.004766671 2167
5       1   OTU.2500    0.004766671 2166


















In [244]:



    


%%R -i comm_richness
# checking assumptions
cat('Target + nonTarget richness = total community richness?: ',
    n.target.genomes + n.nontarget.genomes == comm_richness, '\n')



    


















    








Target + nonTarget richness = total community richness?:  TRUE 


















In [245]:



    


%%R -i workDir
# writing out non-target OTU file
outFile = paste(c(workDir, 'comm_nonTarget.txt'), collapse='/')
write.table(tbl.j, outFile, sep='\t', quote=F, row.names=F)

Randomly selecting amplicon fragment length-GC KDEs from total genome pool





In [246]:



    


# List of non-target OTUs
inFile = os.path.join(workDir, 'comm_nonTarget.txt')
nonTarget = pd.read_csv(inFile, sep='\t')['taxon_name'].tolist()

print 'Number of non-target OTUs: {}'.format(len(nonTarget))
nonTarget[:4]



    


















    






Number of non-target OTUs: 2062










    
Out[246]:








['OTU.11779', 'OTU.9498', 'OTU.3673', 'OTU.493']

















In [260]:



    


# loading amplicon fragments from full genome KDE dataset
inFile = os.path.join(workDir, 'ampFrags.pkl')
ampFrag_target = []
with open(inFile, 'rb') as iFH:
    ampFrag_target = pickle.load(iFH)
print 'Target OTU richness: {}'.format(len(ampFrag_target))



    


















    






Target OTU richness: 108

















In [264]:



    


# loading amplicon fragments from full genome KDE dataset
ampFrag_all = []
with open(ampFragsAllFile, 'rb') as iFH:
    ampFrag_all = pickle.load(iFH)
print 'Count of frag-GC KDEs for all genomes: {}'.format(len(ampFrag_all))



    


















    






Count of frag-GC KDEs for all genomes: 1210

















In [265]:



    


# random selection from list
#target_richness = len(ampFrag_target)

target_richness = len(ampFrag_target)
richness_needed = comm_richness - target_richness
print 'Number of random taxa needed to reach richness: {}'.format(richness_needed)

if richness_needed > 0:
    index = range(target_richness)
    index = np.random.choice(index, richness_needed)
    
    ampFrag_rand = []
    for i in index:
        sys.stderr.write('{},'.format(i))
        ampFrag_rand.append(copy.deepcopy(ampFrag_all[i]))
else:
    ampFrag_rand = []



    


















    






6,1,61,44,12,62,35,52,90,52,49,102,69,23,53,9,24,5,74,5,5,104,6,85,84,38,100,16,48,94,33,74,67,77,84,82,42,44,24,50,97,40,45,50,81,36,99,69,105,36,42,9,91,26,49,3,3,54,1,8,105,96,86,50,7,8,51,30,59,98,19,46,82,48,50,65,59,26,84,97,88,13,0,26,93,70,1,36,65,35,38,61,80,55,58,21,8,52,22,76,47,100,35,90,33,48,96,11,57,4,102,83,96,59,17,82,65,32,65,15,78,54,19,92,60,50,78,32,42,62,87,62,74,83,60,7,78,20,81,13,57,105,21,101,2,74,36,38,11,64,78,58,14,28,107,88,68,8,82,93,103,94,10,80,49,72,64,0,14,83,48,68,61,71,81,68,58,25,5,1,12,18,10,19,6,47,28,107,77,81,36,27,94,87,52,68,25,93,62,106,14,83,73,80,83,87,24,99,59,65,96,10,9,48,70,42,100,55,10,65,13,8,60,63,4,44,97,20,43,79,1,37,40,49,40,106,78,99,58,40,23,69,63,99,52,12,54,99,63,79,32,8,79,90,96,61,38,57,45,78,41,55,27,5,62,101,43,10,21,3,61,64,106,22,11,35,78,98,64,9,8,62,64,28,100,69,49,24,62,101,5,10,91,95,45,3,7,80,57,83,57,15,107,54,0,5,47,43,105,14,7,10,88,58,81,5,105,105,43,53,34,13,65,26,90,49,37,101,54,46,44,16,26,80,83,43,61,107,22,95,92,54,90,58,51,98,61,4,39,88,55,40,88,17,58,104,102,50,72,50,19,3,89,64,74,37,93,7,2,23,46,59,11,28,83,32,93,100,71,55,8,78,61,98,88,41,76,14,90,88,43,20,7,24,68,96,48,28,78,62,80,59,87,11,103,2,79,93,65,51,101,23,84,82,102,86,87,63,90,77,28,5,39,51,107,5,70,18,103,43,33,11,98,12,18,102,18,89,77,90,7,43,52,70,33,88,89,50,32,65,14,41,39,63,42,104,36,1,76,29,45,9,61,74,15,9,89,11,105,75,107,107,91,62,102,52,76,4,69,36,98,90,3,62,56,65,73,21,101,93,83,11,97,107,56,97,92,36,62,55,15,66,97,39,24,48,21,19,104,35,5,1,8,56,60,64,48,103,59,19,53,10,40,80,67,21,71,51,18,68,21,15,51,60,65,50,56,32,15,83,102,2,9,4,94,70,56,82,40,99,8,34,16,32,25,45,30,77,104,60,83,80,66,57,11,87,20,38,34,97,79,73,31,5,49,70,73,80,71,97,82,34,95,98,76,60,86,82,50,2,39,12,75,100,55,10,96,43,95,105,100,86,44,21,107,35,49,56,73,9,38,70,80,3,86,70,79,36,73,45,1,9,24,95,72,60,79,77,98,20,97,106,93,96,14,22,4,81,18,75,90,32,101,98,36,68,89,49,103,15,23,66,62,37,18,40,105,100,78,80,39,41,87,100,58,42,61,5,31,14,6,74,89,63,89,96,28,11,71,18,76,19,25,4,83,35,48,3,94,44,53,81,83,37,8,30,96,47,62,54,61,81,37,1,21,95,76,27,80,57,85,79,21,106,106,94,74,42,102,33,95,100,46,68,85,55,81,37,57,5,84,14,36,60,105,29,92,25,30,29,45,66,30,74,30,12,62,45,97,106,101,66,6,91,103,71,87,3,52,16,81,61,13,46,59,98,23,79,97,45,72,54,77,30,71,1,44,51,87,40,77,89,84,92,99,17,43,48,48,64,104,18,37,24,60,91,46,59,98,82,34,45,87,96,41,92,39,40,8,65,26,79,60,88,94,82,85,5,71,49,65,20,74,18,20,25,70,91,22,47,70,4,40,104,9,107,43,73,61,64,38,46,91,89,70,44,55,98,38,32,71,79,75,48,47,99,26,23,88,45,22,24,1,14,10,61,33,15,98,3,88,90,30,30,65,79,39,60,29,55,12,29,2,76,104,20,36,13,93,91,75,14,62,12,87,21,3,23,44,13,37,82,57,42,46,41,77,43,91,93,45,97,47,29,5,91,48,66,34,106,31,3,84,24,38,99,9,87,48,77,36,0,53,83,46,11,84,21,75,15,66,74,33,85,29,71,28,46,95,68,79,69,75,39,69,33,97,34,39,55,95,46,40,65,91,46,22,43,43,30,8,97,56,0,76,92,90,41,60,1,93,37,39,65,6,21,66,55,56,62,70,9,0,28,73,40,51,60,83,6,95,41,105,78,10,73,9,31,7,77,106,37,27,64,32,35,85,27,19,2,70,1,62,93,105,26,31,44,82,44,85,27,61,3,31,40,82,82,60,53,66,3,61,16,99,98,37,12,18,94,71,11,24,21,48,72,88,44,86,0,31,83,3,20,40,51,5,38,99,12,39,31,48,11,64,32,7,44,98,34,30,21,53,64,105,37,63,20,64,30,29,97,99,18,58,70,38,65,33,70,20,22,75,26,70,97,51,16,0,64,32,22,70,59,28,97,53,4,66,98,3,64,21,2,16,27,99,78,14,52,36,47,10,32,51,84,13,71,94,11,3,100,95,23,70,6,59,103,89,99,75,1,60,61,107,4,59,69,75,16,9,5,70,56,65,15,15,73,106,18,21,24,27,55,28,89,7,84,45,51,104,23,1,60,91,91,67,81,66,89,29,10,100,18,31,61,18,87,90,50,5,1,99,102,91,102,94,107,76,34,42,26,94,66,17,105,96,42,96,21,102,61,68,70,101,93,4,68,31,57,1,35,86,100,46,8,97,21,11,86,73,94,16,62,44,10,34,77,51,5,76,18,43,23,20,70,44,38,4,50,91,54,69,68,92,32,101,41,100,101,69,57,100,3,73,104,103,79,67,87,63,87,37,61,22,20,23,106,48,22,13,87,62,103,60,83,30,72,73,84,92,61,34,87,79,45,9,4,80,12,55,53,31,55,82,100,66,88,78,26,61,25,32,101,87,61,30,6,27,93,74,75,76,21,91,42,31,73,22,0,42,75,52,100,64,57,44,32,92,15,50,26,3,60,55,39,85,96,3,4,83,10,68,89,26,93,14,29,23,15,1,53,81,72,103,76,6,88,46,70,86,65,19,10,71,97,2,15,73,50,69,71,60,11,12,79,42,21,15,77,19,39,80,92,56,56,76,47,27,65,20,43,32,89,22,100,29,107,34,13,78,39,39,54,3,33,20,99,31,46,77,93,70,103,68,65,2,72,65,78,2,15,83,60,69,73,57,74,19,68,54,85,55,96,7,45,91,45,85,93,2,26,60,77,39,75,65,92,32,100,12,96,10,32,84,40,6,37,68,37,10,42,66,74,21,64,43,71,3,62,82,55,81,53,57,53,42,2,72,42,53,22,47,61,83,58,15,71,16,96,7,101,90,14,62,6,97,97,94,102,41,41,1,55,53,86,43,87,87,2,54,88,51,90,68,24,54,50,37,36,30,59,56,31,71,42,9,64,61,61,47,49,62,35,37,26,85,78,107,16,16,39,67,57,62,76,77,33,12,62,73,67,24,30,53,60,106,100,57,55,95,106,41,45,47,53,67,26,89,20,77,92,84,43,94,79,17,71,40,29,79,1,94,8,104,93,19,55,49,59,42,10,26,56,70,19,93,13,79,29,96,15,92,70,82,65,43,37,58,48,65,63,55,88,79,45,71,98,75,68,71,82,75,97,21,7,6,54,4,73,14,64,28,7,11,76,84,13,14,53,37,11,11,90,85,56,3,79,43,31,61,62,73,76,83,40,3,16,51,69,28,63,30,81,29,52,27,66,23,25,84,53,62,92,105,28,45,77,88,7,8,89,72,58,78,35,82,97,9,71,39,95,59,37,82,25,7,49,37,27,63,58,103,69,52,105,41,23,21,40,88,33,58,105,64,76,61,100,17,99,84,51,14,41,65,34,30,57,16,54,53,51,105,38,64,68,17,11,80,54,74,4,79,61,41,72,24,96,23,38,102,29,107,78,102,6,6,102,20,80,23,63,20,71,36,35,78,23,81,19,58,87,27,102,102,42,40,25,53,25,1,80,61,30,6,20,99,104,5,37,103,51,44,62,59,27,38,26,96,48,73,28,55,10,52,37,29,99,85,19,72,52,18,86,9,33,81,53,101,6,64,78,105,97,15,100,37,3,92,46,43,61,60,28,33,96,61,106,27,65,15,63,47,7,63,23,40,0,84,53,44,95,59,93,85,13,87,34,57,14,54,65,18,63,50,66,95,32,105,5,9,9,96,42,9,40,22,8,74,77,73,69,42,91,75,87,90,0,46,59,91,73,67,15,87,84,1,11,15,87,48,105,66,39,93,9,66,2,0,89,60,34,75,56,104,9,13,38,11,67,3,14,46,13,87,91,103,94,28,51,32,16,44,6,93,42,87,95,47,86,40,21,2,45,25,105,15,79,4,15,16,0,42,87,16,71,93,76,92,4,60,28,35,94,18,1,27,62,70,94,97,99,96,76,0,34,11,79,53,84,89,11,35,72,63,82,92,40,38,48,24,80,20,5,106,72,102,98,107,51,15,44,39,56,28,31,27,8,35,66,43,59,97,82,14,81,101,28,70,21,91,59,4,58,18,54,18,28,31,63,14,55,94,93,8,87,30,39,8,30,85,72,









    






Number of random taxa needed to reach richness: 2062

















In [266]:



    


# renaming randomly selected KDEs by non-target OTU-ID
for i in range(len(ampFrag_rand)):
    ampFrag_rand[i][0] = nonTarget[i]



    











In [267]:



    


# appending random taxa to target taxa and writing
outFile = os.path.join(workDir, 'ampFrags_wRand.pkl')

with open(outFile, 'wb') as oFH:
    x = ampFrag_target + ampFrag_rand
    print 'Number of taxa in output: {}'.format(len(x))
    pickle.dump(x, oFH)



    


















    






Number of taxa in output: 2170

Converting fragments to kde object





In [268]:



    


!cd $workDir; \
    SIPSim fragment_kde \
    ampFrags_wRand.pkl \
    > ampFrags_wRand_kde.pkl

Adding diffusion





In [269]:



    


!cd $workDir; \
    SIPSim diffusion \
    ampFrags_wRand_kde.pkl \
    --np $nprocs \
    > ampFrags_wRand_kde_dif.pkl



    


















    






Processing: OTU.5687
Processing: OTU.12484
Processing: OTU.1376
Processing: OTU.3442
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Processing: OTU.2015
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Making an incorp config file





In [270]:



    


!cd $workDir; \
    SIPSim incorpConfigExample \
    --percTaxa 0 \
    --percIncorpUnif 100 \
    > PT0_PI100.config

Adding isotope incorporation to BD distribution





In [271]:



    


!cd $workDir; \
    SIPSim isotope_incorp \
    ampFrags_wRand_kde_dif.pkl \
    PT0_PI100.config \
    --comm comm.txt \
    --np $nprocs \
    > ampFrags_wRand_kde_dif_incorp.pkl



    


















    






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Calculating BD shift from isotope incorporation





In [272]:



    


!cd $workDir; \
    SIPSim BD_shift \
    ampFrags_wRand_kde_dif.pkl \
    ampFrags_wRand_kde_dif_incorp.pkl \
    --np $nprocs \
    > ampFrags_wRand_kde_dif_incorp_BD-shift.txt



    


















    






Loading KDE objects...
Calculating BD shifts...
  Comparing libraries; "NA", "1"
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  Processing: OTU.1110
  Processing: OTU.2287
  Processing: OTU.1635
  Processing: OTU.276
  Processing: OTU.708
  Processing: OTU.1904
  Processing: OTU.552
  Processing: OTU.555
  Processing: OTU.1765
  Processing: OTU.2124
  Processing: OTU.21
  Processing: OTU.12
  Processing: OTU.664
  Processing: OTU.7694
  Processing: OTU.2131
  Processing: OTU.926
  Processing: OTU.5838
  Processing: OTU.8508
  Processing: OTU.2043
  Processing: OTU.6591
  Processing: OTU.351
  Processing: OTU.76
  Processing: OTU.1113
  Processing: OTU.8356
  Processing: OTU.732
  Processing: OTU.2627
  Processing: OTU.278
  Processing: OTU.1569
  Processing: OTU.6439
  Processing: OTU.2074
  Processing: OTU.2127
  Processing: OTU.7697
  Processing: OTU.663
  Processing: OTU.22
  Processing: OTU.15
  Processing: OTU.5587
  Processing: OTU.4262
  Processing: OTU.2040
  Processing: OTU.3241
  Processing: OTU.2615
  Processing: OTU.5915
  Processing: OTU.1114
  Processing: OTU.1931
  Processing: OTU.735
  Processing: OTU.2625
  Processing: OTU.6819
  Processing: OTU.4049
  Processing: OTU.279
  Processing: OTU.1561
  Processing: OTU.1229
  Processing: OTU.12603
  Processing: OTU.863
  Processing: OTU.23
  Processing: OTU.512
  Processing: OTU.662
  Processing: OTU.14
  Processing: OTU.3062
  Processing: OTU.1344
  Processing: OTU.7056
  Processing: OTU.5914
  Processing: OTU.1903
  Processing: OTU.484
  Processing: OTU.495
  Processing: OTU.1228
  Processing: OTU.1117
  Processing: OTU.1562
  Processing: OTU.1039
  Processing: OTU.1032
  Processing: OTU.10405
  Processing: OTU.6746
  Processing: OTU.11411
  Processing: OTU.4983
  Processing: OTU.2019
  Processing: OTU.2078
  Processing: OTU.6612
  Processing: OTU.661
  Processing: OTU.3060
  Processing: OTU.1345
  Processing: OTU.17
  Processing: OTU.5917
  Processing: OTU.1225
  Processing: OTU.320
  Processing: OTU.737
  Processing: OTU.6581
  Processing: OTU.1563
  Processing: OTU.483
  Processing: OTU.7776
  Processing: OTU.3477
  Processing: OTU.6741
  Processing: OTU.1033
  Processing: OTU.3406
  Processing: OTU.792
  Processing: OTU.1028
  Processing: OTU.2599
  Processing: OTU.6616
  Processing: OTU.4467
  Processing: OTU.660
  Processing: OTU.1346
  Processing: OTU.865
  Processing: OTU.16
  Processing: OTU.4318
  Processing: OTU.8167
  Processing: OTU.736
  Processing: OTU.497
  Processing: OTU.7401
  Processing: OTU.1565
  Processing: OTU.102
  Processing: OTU.482
  Processing: OTU.1576
  Processing: OTU.1118
  Processing: OTU.1030
  Processing: OTU.1026
  Processing: OTU.8887
  Processing: OTU.3065
  Processing: OTU.3084
  Processing: OTU.4268
  Processing: OTU.8375
  Processing: OTU.1105
  Processing: OTU.6176
  Processing: OTU.864
  Processing: OTU.649
  Processing: OTU.19
  Processing: OTU.739
  Processing: OTU.490
  Processing: OTU.1566
  Processing: OTU.103
  Processing: OTU.11187
  Processing: OTU.5909
  Processing: OTU.1575
  Processing: OTU.3988
  Processing: OTU.1393
  Processing: OTU.658
  Processing: OTU.1021
  Processing: OTU.6763
  Processing: OTU.7337
  Processing: OTU.14094
  Processing: OTU.2931
  Processing: OTU.5820
  Processing: OTU.3087
  Processing: OTU.1072
  Processing: OTU.648
  Processing: OTU.867
  Processing: OTU.738
  Processing: OTU.1823
  Processing: OTU.803
  Processing: OTU.5152
  Processing: OTU.492
  Processing: OTU.453
  Processing: OTU.8172
  Processing: OTU.810
  Processing: OTU.1020
  Processing: OTU.1520
  Processing: OTU.4310
  Processing: OTU.3190
  Processing: OTU.325
  Processing: OTU.8756
  Processing: OTU.1681
  Processing: OTU.1895
  Processing: OTU.5228
  Processing: OTU.2637
  Processing: OTU.1753
  Processing: OTU.399
  Processing: OTU.2920
  Processing: OTU.2058
  Processing: OTU.493
  Processing: OTU.4730
  Processing: OTU.106
  Processing: OTU.3452
  Processing: OTU.3324
  Processing: OTU.3038
  Processing: OTU.1022
  Processing: OTU.9207
  Processing: OTU.11751
  Processing: OTU.3682
  Processing: OTU.5691
  Processing: OTU.2442
  Processing: OTU.2836
  Processing: OTU.1683
  Processing: OTU.43
  Processing: OTU.2633
  Processing: OTU.801
  Processing: OTU.3083
  Processing: OTU.398
  Processing: OTU.2923
  Processing: OTU.498
  Processing: OTU.7789
  Processing: OTU.12461
  Processing: OTU.3328
  Processing: OTU.1711
  Processing: OTU.5218
  Processing: OTU.6143
  Processing: OTU.813
  Processing: OTU.478
  Processing: OTU.215
  Processing: OTU.728
  Processing: OTU.9366
  Processing: OTU.1685
  Processing: OTU.5116
  Processing: OTU.807
  Processing: OTU.587
  Processing: OTU.641
  Processing: OTU.1219
  Processing: OTU.499
  Processing: OTU.323
  Processing: OTU.12079
  Processing: OTU.107
  Processing: OTU.36
  Processing: OTU.7237
  Processing: OTU.1713
  Processing: OTU.3392
  Processing: OTU.2447
  Processing: OTU.814
  Processing: OTU.726
  Processing: OTU.1235
  Processing: OTU.3274
  Processing: OTU.585
  Processing: OTU.11522
  Processing: OTU.9164
  Processing: OTU.806
  Processing: OTU.2925
  Processing: OTU.7191
  Processing: OTU.392
  Processing: OTU.104
  Processing: OTU.4677
  Processing: OTU.4673
  Processing: OTU.4706
  Processing: OTU.628
  Processing: OTU.5428
  Processing: OTU.7756
  Processing: OTU.472
  Processing: OTU.2029
  Processing: OTU.724
  Processing: OTU.1236
  Processing: OTU.3272
  Processing: OTU.6332
  Processing: OTU.805
  Processing: OTU.4835
  Processing: OTU.380
  Processing: OTU.8364
  Processing: OTU.6344
  Processing: OTU.391
  Processing: OTU.2030
  Processing: OTU.682
  Processing: OTU.9978
  Processing: OTU.4074
  Processing: OTU.3156
  Processing: OTU.546
  Processing: OTU.473
  Processing: OTU.549
  Processing: OTU.816
  Processing: OTU.725
  Processing: OTU.1237
  Processing: OTU.335
  Processing: OTU.804
  Processing: OTU.582
  Processing: OTU.5119
  Processing: OTU.381
  Processing: OTU.7353
  Processing: OTU.390
  Processing: OTU.7071
  Processing: OTU.457
  Processing: OTU.1597
  Processing: OTU.2156
  Processing: OTU.7977
  Processing: OTU.2448
  Processing: OTU.471
  Processing: OTU.547
  Processing: OTU.817
  Processing: OTU.3216
  Processing: OTU.11409
  Processing: OTU.7124
  Processing: OTU.722
  Processing: OTU.808
  Processing: OTU.851
  Processing: OTU.6110
  Processing: OTU.1804
  Processing: OTU.1596
  Processing: OTU.5106
  Processing: OTU.3035
  Processing: OTU.5118
  Processing: OTU.382
  Processing: OTU.7973
  Processing: OTU.2151
  Processing: OTU.474
  Processing: OTU.623
  Processing: OTU.819
  Processing: OTU.3271
  Processing: OTU.1542
  Processing: OTU.2584
  Processing: OTU.2900
  Processing: OTU.723
  Processing: OTU.1590
  Processing: OTU.1598
  Processing: OTU.644
  Processing: OTU.1803
  Processing: OTU.5105
  Processing: OTU.12515
  Processing: OTU.11643
  Processing: OTU.6642
  Processing: OTU.383
  Processing: OTU.13701
  Processing: OTU.475
  Processing: OTU.2158
  Processing: OTU.622
  Processing: OTU.2027
  Processing: OTU.1630
  Processing: OTU.4245
  Processing: OTU.3058
  Processing: OTU.1543
  Processing: OTU.9211
  Processing: OTU.720
  Processing: OTU.1352
  Processing: OTU.395
  Processing: OTU.1802
  Processing: OTU.9115
  Processing: OTU.1830
  Processing: OTU.9782
  Processing: OTU.39
  Processing: OTU.384
  Processing: OTU.828
  Processing: OTU.6253
  Processing: OTU.620
  Processing: OTU.2020
  Processing: OTU.356
  Processing: OTU.3056
  Processing: OTU.1350
  Processing: OTU.626
  Processing: OTU.646
  Processing: OTU.8981
  Processing: OTU.1801
  Processing: OTU.721
  Processing: OTU.1164
  Processing: OTU.1836
  Processing: OTU.3033
  Processing: OTU.38
  Processing: OTU.6102
  Processing: OTU.1176
  Processing: OTU.627
  Processing: OTU.2309
  Processing: OTU.2023
  Processing: OTU.4242
  Processing: OTU.3057
  Processing: OTU.1357
  Processing: OTU.1769
  Processing: OTU.1582
  Processing: OTU.281
  Processing: OTU.2330
  Processing: OTU.6385
  Processing: OTU.4405
  Processing: OTU.1837
  Processing: OTU.13492
  Processing: OTU.642
  Processing: OTU.3461
  Processing: OTU.1175
  Processing: OTU.232
  Processing: OTU.3043
  Processing: OTU.8188
  Processing: OTU.1355
  Processing: OTU.355
  Processing: OTU.178
  Processing: OTU.249
  Processing: OTU.248
  Processing: OTU.4856
  Processing: OTU.1583
  Processing: OTU.280
  Processing: OTU.2331
  Processing: OTU.1166
  Processing: OTU.1834
  Processing: OTU.32
  Processing: OTU.8094
  Processing: OTU.387
  Processing: OTU.1173
  Processing: OTU.625
  Processing: OTU.1354
  Processing: OTU.1911
  Processing: OTU.6030
  Processing: OTU.1288
  Processing: OTU.7210
  Processing: OTU.245
  Processing: OTU.1580
  Processing: OTU.283
  Processing: OTU.2333
  Processing: OTU.1167
  Processing: OTU.853
  Processing: OTU.31
  Processing: OTU.1366
  Processing: OTU.7511
  Processing: OTU.2039
  Processing: OTU.5857
  Processing: OTU.1349
  Processing: OTU.3045
  Processing: OTU.1696
  Processing: OTU.7213
  Processing: OTU.1910
  Processing: OTU.244
  Processing: OTU.7759
  Processing: OTU.1163
  Processing: OTU.282
  Processing: OTU.5454
  Processing: OTU.13643
  Processing: OTU.258
  Processing: OTU.1367
  Processing: OTU.2807
  Processing: OTU.4411
  Processing: OTU.354
  Processing: OTU.3516
  Processing: OTU.233
  Processing: OTU.2456
  Processing: OTU.1917
  Processing: OTU.1760
  Processing: OTU.1168
  Processing: OTU.1584
  Processing: OTU.285
  Processing: OTU.2335
  Processing: OTU.259
  Processing: OTU.13393
  Processing: OTU.8572
  Processing: OTU.1364
  Processing: OTU.1692
  Processing: OTU.3185
  Processing: OTU.3519
  Processing: OTU.1170
  Processing: OTU.1916
  Processing: OTU.246
  Processing: OTU.1169
  Processing: OTU.284
  Processing: OTU.2336
  Processing: OTU.252
  Processing: OTU.6813
  Processing: OTU.4665
  Processing: OTU.1365
  Processing: OTU.2459
  Processing: OTU.7074
  Processing: OTU.538
  Processing: OTU.8616
  Processing: OTU.14045
  Processing: OTU.2337
  Processing: OTU.2487
  Processing: OTU.519
  Processing: OTU.287
  Processing: OTU.253
  Processing: OTU.4667
  Processing: OTU.605
  Processing: OTU.1362
  Processing: OTU.1179
  Processing: OTU.3135
  Processing: OTU.5072
  Processing: OTU.9686
  Processing: OTU.251
  Processing: OTU.2038
  Processing: OTU.2483
  Processing: OTU.5018
  Processing: OTU.656
  Processing: OTU.654
  Processing: OTU.1361
  Processing: OTU.13038
  Processing: OTU.5071
  Processing: OTU.256
  Processing: OTU.825
  Processing: OTU.2481
  Processing: OTU.776
  Processing: OTU.5845
  Processing: OTU.5724
  Processing: OTU.1544
  Processing: OTU.257
  Processing: OTU.536
  Processing: OTU.6327
  Processing: OTU.2811
  Processing: OTU.652
  Processing: OTU.1615
  Processing: OTU.5679
  Processing: OTU.255
  Processing: OTU.535
  Processing: OTU.4214
  Processing: OTU.1368
  Processing: OTU.653
  Processing: OTU.4933
  Processing: OTU.6111
  Processing: OTU.222
  Processing: OTU.1571
  Processing: OTU.6115
  Processing: OTU.2034
  Processing: OTU.6864
  Processing: OTU.650
  Processing: OTU.533
  Processing: OTU.5674
  Processing: OTU.1825
  Processing: OTU.4934
  Processing: OTU.6861
  Processing: OTU.651
  Processing: OTU.7685
  Processing: OTU.532
  Processing: OTU.3858
  Processing: OTU.820
  Processing: OTU.1821
  Processing: OTU.6013
  Processing: OTU.3192
  Processing: OTU.1217
  Processing: OTU.46
  Processing: OTU.823
  Processing: OTU.1820
  Processing: OTU.8895
  Processing: OTU.12499
  Processing: OTU.1214
  Processing: OTU.530
  Processing: OTU.8783
  Processing: OTU.946
  Processing: OTU.1215
  Processing: OTU.234
  Processing: OTU.11083
  Processing: OTU.543
  Processing: OTU.8415

Simulating gradient fractions





In [273]:



    


!cd $workDir; \
    SIPSim gradient_fractions \
    comm.txt \
    > fracs.txt

Simulating an OTU table





In [666]:



    


!cd $workDir; \
    SIPSim OTU_table \
    ampFrags_wRand_kde_dif_incorp.pkl \
    comm.txt \
    fracs.txt \
    --abs 1e9 \
    --np $nprocs \
    > OTU_abs1e9.txt



    


















    






Loading files...
Simulating OTUs...
Processing library: "1"
  Processing taxon: "OTU.22"
   taxon abs-abundance:  24310024
  Processing taxon: "OTU.43"
   taxon abs-abundance:  5338672
  Processing taxon: "OTU.81"
   taxon abs-abundance:  3289003
  Processing taxon: "OTU.116"
   taxon abs-abundance:  2526336
  Processing taxon: "OTU.17"
   taxon abs-abundance:  1859002
  Processing taxon: "OTU.66"
   taxon abs-abundance:  1573002
  Processing taxon: "OTU.8846"
   taxon abs-abundance:  1382335
  Processing taxon: "OTU.149"
   taxon abs-abundance:  1096334
  Processing taxon: "OTU.107"
   taxon abs-abundance:  1001001
  Processing taxon: "OTU.6861"
   taxon abs-abundance:  810334
  Processing taxon: "OTU.470"
   taxon abs-abundance:  715001
  Processing taxon: "OTU.3355"
   taxon abs-abundance:  619667
  Processing taxon: "OTU.5691"
   taxon abs-abundance:  572001
  Processing taxon: "OTU.194"
   taxon abs-abundance:  1096334
  Processing taxon: "OTU.121"
   taxon abs-abundance:  1573002
  Processing taxon: "OTU.428"
   taxon abs-abundance:  1001001
  Processing taxon: "OTU.429"
   taxon abs-abundance:  810334
  Processing taxon: "OTU.409"
   taxon abs-abundance:  1859002
  Processing taxon: "OTU.3156"
   taxon abs-abundance:  715001
  Processing taxon: "OTU.294"
   taxon abs-abundance:  476667
  Processing taxon: "OTU.4938"
   taxon abs-abundance:  619667
  Processing taxon: "OTU.616"
   taxon abs-abundance:  1334668
  Processing taxon: "OTU.436"
   taxon abs-abundance:  429000
  Processing taxon: "OTU.7536"
   taxon abs-abundance:  2526336
  Processing taxon: "OTU.725"
   taxon abs-abundance:  429000
  Processing taxon: "OTU.419"
   taxon abs-abundance:  476667
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.276"
   taxon abs-abundance:  476667
  Processing taxon: "OTU.3190"
   taxon abs-abundance:  715001
  Processing taxon: "OTU.539"
   taxon abs-abundance:  429000
  Processing taxon: "OTU.5683"
   taxon abs-abundance:  810334
  Processing taxon: "OTU.356"
  Processing taxon: "OTU.399"
   taxon abs-abundance:  619667
   taxon abs-abundance:  381334
  Processing taxon: "OTU.162"
  Processing taxon: "OTU.7040"
   taxon abs-abundance:  1096334
   taxon abs-abundance:  572001
  Processing taxon: "OTU.6358"
   taxon abs-abundance:  953334
  Processing taxon: "OTU.326"
   taxon abs-abundance:  381334
  Processing taxon: "OTU.3328"
   taxon abs-abundance:  333667
  Processing taxon: "OTU.1583"
   taxon abs-abundance:  476667
  Processing taxon: "OTU.421"
   taxon abs-abundance:  429000
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.1712"
   taxon abs-abundance:  429000
  Processing taxon: "OTU.310"
   taxon abs-abundance:  333667
  Processing taxon: "OTU.10167"
  Processing taxon: "OTU.478"
   taxon abs-abundance:  333667
   taxon abs-abundance:  381334
  Processing taxon: "OTU.5587"
   taxon abs-abundance:  715001
  Processing taxon: "OTU.6407"
   taxon abs-abundance:  619667
  Processing taxon: "OTU.4204"
   taxon abs-abundance:  1525335
  Processing taxon: "OTU.6013"
   taxon abs-abundance:  286000
  Processing taxon: "OTU.329"
   taxon abs-abundance:  476667
  Processing taxon: "OTU.161"
   taxon abs-abundance:  810334
  Processing taxon: "OTU.317"
  Processing taxon: "OTU.747"
  Processing taxon: "OTU.7851"
   taxon abs-abundance:  429000
   taxon abs-abundance:  381334
   taxon abs-abundance:  333667
  Processing taxon: "OTU.24"
   taxon abs-abundance:  3289003
  Processing taxon: "OTU.505"
   taxon abs-abundance:  333667
  Processing taxon: "OTU.8111"
   taxon abs-abundance:  381334
  Processing taxon: "OTU.982"
   taxon abs-abundance:  286000
  Processing taxon: "OTU.42"
   taxon abs-abundance:  1811335
  Processing taxon: "OTU.12027"
   taxon abs-abundance:  953334
  Processing taxon: "OTU.213"
   taxon abs-abundance:  333667
  Processing taxon: "OTU.127"
   taxon abs-abundance:  1096334
  Processing taxon: "OTU.543"
   taxon abs-abundance:  476667
  Processing taxon: "OTU.204"
   taxon abs-abundance:  429000
  Processing taxon: "OTU.201"
  Processing taxon: "OTU.384"
   taxon abs-abundance:  333667
   taxon abs-abundance:  572001
  Processing taxon: "OTU.10129"
   taxon abs-abundance:  619667
  Processing taxon: "OTU.1417"
   taxon abs-abundance:  286000
  Processing taxon: "OTU.264"
   taxon abs-abundance:  715001
  Processing taxon: "OTU.642"
   taxon abs-abundance:  381334
  Processing taxon: "OTU.6783"
   taxon abs-abundance:  333667
  Processing taxon: "OTU.726"
   taxon abs-abundance:  381334
  Processing taxon: "OTU.666"
   taxon abs-abundance:  286000
  Processing taxon: "OTU.484"
   taxon abs-abundance:  810334
  Processing taxon: "OTU.5875"
   taxon abs-abundance:  333667
  Processing taxon: "OTU.867"
  Processing taxon: "OTU.340"
   taxon abs-abundance:  476667
   taxon abs-abundance:  429000
  Processing taxon: "OTU.535"
   taxon abs-abundance:  381334
  Processing taxon: "OTU.6616"
   taxon abs-abundance:  333667
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.402"
   taxon abs-abundance:  333667
  Processing taxon: "OTU.4245"
   taxon abs-abundance:  286000
  Processing taxon: "OTU.275"
   taxon abs-abundance:  619667
  Processing taxon: "OTU.592"
   taxon abs-abundance:  333667
  Processing taxon: "OTU.179"
   taxon abs-abundance:  953334
  Processing taxon: "OTU.258"
   taxon abs-abundance:  715001
  Processing taxon: "OTU.351"
   taxon abs-abundance:  429000
  Processing taxon: "OTU.8432"
   taxon abs-abundance:  381334
  Processing taxon: "OTU.100"
  Processing taxon: "OTU.57"
   taxon abs-abundance:  1334668
   taxon abs-abundance:  2478669
  Processing taxon: "OTU.1830"
  Processing taxon: "OTU.180"
   taxon abs-abundance:  333667
   taxon abs-abundance:  286000
  Processing taxon: "OTU.63"
  Processing taxon: "OTU.6217"
   taxon abs-abundance:  5100338
   taxon abs-abundance:  1525335
  Processing taxon: "OTU.7381"
   taxon abs-abundance:  476667
  Processing taxon: "OTU.4922"
   taxon abs-abundance:  1096334
  Processing taxon: "OTU.4038"
   taxon abs-abundance:  333667
  Processing taxon: "OTU.2256"
   taxon abs-abundance:  381334
  Processing taxon: "OTU.11322"
  Processing taxon: "OTU.6450"
   taxon abs-abundance:  572001
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.542"
   taxon abs-abundance:  810334
   taxon abs-abundance:  572001
  Processing taxon: "OTU.6966"
   taxon abs-abundance:  286000
  Processing taxon: "OTU.111"
   taxon abs-abundance:  333667
  Processing taxon: "OTU.314"
   taxon abs-abundance:  381334
  Processing taxon: "OTU.6439"
   taxon abs-abundance:  619667
  Processing taxon: "OTU.235"
   taxon abs-abundance:  429000
  Processing taxon: "OTU.843"
   taxon abs-abundance:  333667
  Processing taxon: "OTU.288"
   taxon abs-abundance:  476667
  Processing taxon: "OTU.5118"
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   WARNING: No bins for taxon; likely caused by no BD KDE
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   taxon abs-abundance:  4719005
  Processing taxon: "OTU.91"
   taxon abs-abundance:  1668335
  Processing taxon: "OTU.200"
   taxon abs-abundance:  1906669
  Processing taxon: "OTU.47"
   taxon abs-abundance:  2812336
  Processing taxon: "OTU.4164"
   taxon abs-abundance:  1620668
  Processing taxon: "OTU.176"
   taxon abs-abundance:  1906669
  Processing taxon: "OTU.59"
   taxon abs-abundance:  1620668
  Processing taxon: "OTU.88"
   taxon abs-abundance:  4671338
  Processing taxon: "OTU.79"
   taxon abs-abundance:  2764669
  Processing taxon: "OTU.4467"
   taxon abs-abundance:  1620668
  Processing taxon: "OTU.131"
   taxon abs-abundance:  1906669
  Processing taxon: "OTU.20"
   taxon abs-abundance:  18923686
  Processing taxon: "OTU.7650"
   taxon abs-abundance:  1620668
  Processing taxon: "OTU.5848"
   taxon abs-abundance:  1906669
  Processing taxon: "OTU.7227"
   taxon abs-abundance:  2717003
  Processing taxon: "OTU.11522"
   taxon abs-abundance:  1620668
  Processing taxon: "OTU.25"
   taxon abs-abundance:  4576005
  Processing taxon: "OTU.3911"
   taxon abs-abundance:  1906669
  Processing taxon: "OTU.408"
   taxon abs-abundance:  1620668
  Processing taxon: "OTU.29"
   taxon abs-abundance:  2669336
  Processing taxon: "OTU.5845"
   taxon abs-abundance:  1859002
  Processing taxon: "OTU.80"
   taxon abs-abundance:  1573002
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.5714"
   taxon abs-abundance:  1573002
  Processing taxon: "OTU.4663"
   taxon abs-abundance:  2669336
  Processing taxon: "OTU.132"
   taxon abs-abundance:  1859002
  Processing taxon: "OTU.46"
   taxon abs-abundance:  4433004
  Processing taxon: "OTU.5712"
   taxon abs-abundance:  1859002
  Processing taxon: "OTU.2502"
   taxon abs-abundance:  2669336
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.48"
   taxon abs-abundance:  2669336
  Processing taxon: "OTU.118"
   taxon abs-abundance:  1859002
  Processing taxon: "OTU.6885"
   taxon abs-abundance:  4433004
  Processing taxon: "OTU.2428"
   taxon abs-abundance:  2669336
  Processing taxon: "OTU.2265"
   taxon abs-abundance:  2621669
  Processing taxon: "OTU.26"
   taxon abs-abundance:  4433004
  Processing taxon: "OTU.240"
   taxon abs-abundance:  2621669
  Processing taxon: "OTU.2"
   taxon abs-abundance:  16826350
  Processing taxon: "OTU.16"
   taxon abs-abundance:  2621669
  Processing taxon: "OTU.8395"
   taxon abs-abundance:  4337671
  Processing taxon: "OTU.53"
   taxon abs-abundance:  2574003
  Processing taxon: "OTU.27"
   taxon abs-abundance:  2574003
  Processing taxon: "OTU.64"
   taxon abs-abundance:  4337671
  Processing taxon: "OTU.3517"
   taxon abs-abundance:  2526336
  Processing taxon: "OTU.4429"
   taxon abs-abundance:  3956337
  Processing taxon: "OTU.4659"
   taxon abs-abundance:  3861004
  Processing taxon: "OTU.108"
   taxon abs-abundance:  15777682
  Processing taxon: "OTU.67"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.76"
   taxon abs-abundance:  3765670
  Processing taxon: "OTU.11"
   taxon abs-abundance:  3718004
  Processing taxon: "OTU.49"
   taxon abs-abundance:  3527337
  Processing taxon: "OTU.139"
   taxon abs-abundance:  3479670
  Processing taxon: "OTU.8"
   taxon abs-abundance:  12012012
  Processing taxon: "OTU.125"
   taxon abs-abundance:  3432003
  Processing taxon: "OTU.4"
   taxon abs-abundance:  3432003
  Processing taxon: "OTU.58"
   taxon abs-abundance:  3384337
  Processing taxon: "OTU.3"
   taxon abs-abundance:  11964345
  Processing taxon: "OTU.2949"
   taxon abs-abundance:  3336670
  Processing taxon: "OTU.85"
   taxon abs-abundance:  3336670
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.21"
   taxon abs-abundance:  11916679
  Processing taxon: "OTU.13"
   taxon abs-abundance:  9581010
  Processing taxon: "OTU.7"
   taxon abs-abundance:  9581010
  Processing taxon: "OTU.32"
   taxon abs-abundance:  8389342
  Processing taxon: "OTU.14"
   taxon abs-abundance:  8246342
  Processing taxon: "OTU.19"
   taxon abs-abundance:  7912675
  Processing taxon: "OTU.30"
   taxon abs-abundance:  7293007
  Processing taxon: "OTU.40"
   taxon abs-abundance:  7102340
  Processing taxon: "OTU.39"
   taxon abs-abundance:  6578007
  Processing taxon: "OTU.60"
   taxon abs-abundance:  6578007
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.12"
   taxon abs-abundance:  6292006
  Processing taxon: "OTU.3608"
   taxon abs-abundance:  6292006
  Processing taxon: "OTU.69"
   taxon abs-abundance:  6244340
  Processing taxon: "OTU.9"
   taxon abs-abundance:  6244340
  Processing taxon: "OTU.2176"
   taxon abs-abundance:  6149006
  Processing taxon: "OTU.37"
   taxon abs-abundance:  5863006
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.1597"
   taxon abs-abundance:  5815339
  Processing taxon: "OTU.71"
   taxon abs-abundance:  5672339
  Processing taxon: "OTU.4907"
   taxon abs-abundance:  5481672
  Processing taxon: "OTU.6967"
   taxon abs-abundance:  5481672
  Processing taxon: "OTU.36"
   taxon abs-abundance:  5386339

Plotting taxon abundances





In [673]:



    


%%R -i workDir
setwd(workDir)

# loading file
tbl = read.delim('OTU_abs1e9.txt', sep='\t')



    











In [674]:



    


%%R
## BD for G+C of 0 or 100
BD.GCp0 = 0 * 0.098 + 1.66
BD.GCp100 = 1 * 0.098 + 1.66



    











In [675]:



    


%%R -w 800 -h 300
# plotting absolute abundances

tbl.s = tbl %>%
    group_by(library, BD_mid) %>%
    summarize(total_count = sum(count))

## plot
p = ggplot(tbl.s, aes(BD_mid, total_count)) +
    geom_area(stat='identity', alpha=0.3, position='dodge') +
    geom_histogram(stat='identity') +
    geom_vline(xintercept=c(BD.GCp0, BD.GCp100), linetype='dashed', alpha=0.5) +
    labs(x='Buoyant density') +
    theme_bw() +
    theme( 
        text = element_text(size=16) 
    )
p



    


















    
























In [676]:



    


%%R -w 800 -h 300
# plotting number of taxa at each BD

tbl.nt = tbl %>%
    filter(count > 0) %>%
    group_by(library, BD_mid) %>%
    summarize(n_taxa = n())

## plot
p = ggplot(tbl.nt, aes(BD_mid, n_taxa)) +
    geom_area(stat='identity', alpha=0.3, position='dodge') +
    geom_histogram(stat='identity') +
    geom_vline(xintercept=c(BD.GCp0, BD.GCp100), linetype='dashed', alpha=0.5) +
    labs(x='Buoyant density', y='Number of taxa') +
    theme_bw() +
    theme( 
        text = element_text(size=16),
        legend.position = 'none'
    )
p



    


















    
























In [677]:



    


%%R -w 800 -h 250
# plotting relative abundances

## plot
p = ggplot(tbl, aes(BD_mid, count, fill=taxon)) +
    geom_vline(xintercept=c(BD.GCp0, BD.GCp100), linetype='dashed', alpha=0.5) +
    labs(x='Buoyant density') +
    theme_bw() +
    theme( 
        text = element_text(size=16),
        legend.position = 'none'
    )
p + geom_area(stat='identity', position='dodge', alpha=0.5)



    


















    
























In [678]:



    


%%R -w 800 -h 250

p + geom_area(stat='identity', position='fill')

Subsampling from the OTU table





In [680]:



    


dist,loc,scale = seq_per_fraction

!cd $workDir; \
    SIPSim OTU_subsample \
    --dist $dist \
    --dist_params mean:$loc,sigma:$scale \
    --min_size 10000 \
    --max_size 100000 \
    --walk 1 \
    OTU_abs1e9.txt \
    > OTU_abs1e9_sub.txt

Testing/Plotting seq count distribution of subsampled fraction samples





In [681]:



    


%%R -h 300
setwd(workDir)

tbl = read.csv('OTU_abs1e9_sub.txt', sep='\t') 

tbl.s = tbl %>% 
    group_by(library, fraction) %>%
    summarize(total_count = sum(count)) %>%
    ungroup() %>%
    mutate(library = as.character(library))

ggplot(tbl.s, aes(total_count)) +
    geom_density(fill='blue')



    


















    
























In [682]:



    


%%R -h 300 -w 600
setwd(workDir)

tbl.s = tbl %>%
    group_by(fraction, BD_min, BD_mid, BD_max) %>%
    summarize(total_count = sum(count)) 

ggplot(tbl.s, aes(BD_mid, total_count)) +
    geom_point() +
    geom_line() +
    labs(x='Buoyant density', y='Total sequences') +
    theme_bw() +
    theme(
        text = element_text(size=16)
        )



    


















    
























In [683]:



    


%%R -w 800 -h 300
# plotting number of taxa at each BD

tbl.nt = tbl %>%
    filter(count > 0) %>%
    group_by(library, fraction, BD_mid) %>%
    summarize(n_taxa = n())

## plot
ggplot(tbl.nt, aes(BD_mid, n_taxa)) +
    geom_area(stat='identity', alpha=0.5) +
    geom_point() +
    geom_vline(xintercept=c(BD.GCp0, BD.GCp100), linetype='dashed', alpha=0.5) +
    labs(x='Buoyant density', y='Number of taxa') +
    theme_bw() +
    theme( 
        text = element_text(size=16),
        legend.position = 'none'
    )

Getting list of target taxa





In [684]:



    


%%R -i workDir

inFile = paste(c(workDir, 'target_genome_index.txt'), collapse='/')

tbl.target = read.delim(inFile, sep='\t', header=F)
colnames(tbl.target) = c('OTUId', 'genome_file', 'genome_ID', 'X', 'Y', 'Z')
tbl.target = tbl.target %>% distinct(OTUId)


cat('Number of target OTUs: ', tbl.target$OTUId %>% unique %>% length, '\n')
cat('----------\n')
tbl.target %>% head(n=3)



    


















    








Number of target OTUs:  108 
----------
     OTUId
1 OTU.1457
2   OTU.77
3 OTU.2347
                                                                                       genome_file
1    /home/nick/notebook/SIPSim/dev/bac_genome1210/genomes/Thermomonospora_curvata_DSM_43183.fasta
2      /home/nick/notebook/SIPSim/dev/bac_genome1210/genomes/Pseudoxanthomonas_spadix_BD-a59.fasta
3 /home/nick/notebook/SIPSim/dev/bac_genome1210/genomes/Micromonospora_aurantiaca_ATCC_27029.fasta
                                      genome_ID X           Y    Z
1    CP001738_Thermomonospora_curvata_DSM_43183 1 0.009533343 1038
2      CP003093_Pseudoxanthomonas_spadix_BD_a59 1 0.019066686  700
3 CP002162_Micromonospora_aurantiaca_ATCC_27029 1 0.004766671 1380

Plotting abundance distributions





In [685]:



    


%%R -w 800 -h 250
# plotting relative abundances

tbl = tbl %>% 
    group_by(fraction) %>%
    mutate(rel_abund = count / sum(count))


## plot
p = ggplot(tbl, aes(BD_mid, count, fill=taxon)) +
    geom_vline(xintercept=c(BD.GCp0, BD.GCp100), linetype='dashed', alpha=0.5) +
    labs(x='Buoyant density') +
    theme_bw() +
    theme( 
        text = element_text(size=16),
        legend.position = 'none'
    )
p + geom_area(stat='identity', position='dodge', alpha=0.5)



    


















    
























In [686]:



    


%%R -w 800 -h 250

p = ggplot(tbl, aes(BD_mid, rel_abund, fill=taxon)) +
    geom_vline(xintercept=c(BD.GCp0, BD.GCp100), linetype='dashed', alpha=0.5) +
    labs(x='Buoyant density') +
    theme_bw() +
    theme( 
        text = element_text(size=16),
        legend.position = 'none'
    )
p + geom_area(stat='identity')

Abundance distribution of just target taxa





In [687]:



    


%%R

targets = tbl.target$OTUId %>% as.vector %>% unique 

tbl.f = tbl %>%
    filter(taxon %in% targets)

tbl.f %>% head



    


















    








Source: local data frame [6 x 8]
Groups: fraction

  library    fraction taxon BD_min BD_mid BD_max count    rel_abund
1       1  -inf-1.660 OTU.1   -Inf  1.659  1.659    19 0.0013704559
2       1 1.660-1.664 OTU.1  1.660  1.662  1.664     4 0.0002569868
3       1 1.664-1.666 OTU.1  1.664  1.665  1.666     0 0.0000000000
4       1 1.666-1.673 OTU.1  1.666  1.669  1.673     0 0.0000000000
5       1 1.673-1.680 OTU.1  1.673  1.676  1.680     0 0.0000000000
6       1 1.680-1.685 OTU.1  1.680  1.683  1.685     3 0.0001528273


















In [688]:



    


%%R -w 800 -h 250
# plotting absolute abundances

## plot
p = ggplot(tbl.f, aes(BD_mid, count, fill=taxon)) +
    geom_vline(xintercept=c(BD.GCp0, BD.GCp100), linetype='dashed', alpha=0.5) +
    labs(x='Buoyant density') +
    theme_bw() +
    theme( 
        text = element_text(size=16),
        legend.position = 'none'
    )
p + geom_area(stat='identity', position='dodge', alpha=0.5)



    


















    
























In [689]:



    


%%R -w 800 -h 250
# plotting relative abundances

p = ggplot(tbl.f, aes(BD_mid, rel_abund, fill=taxon)) +
    geom_vline(xintercept=c(BD.GCp0, BD.GCp100), linetype='dashed', alpha=0.5) +
    labs(x='Buoyant density') +
    theme_bw() +
    theme( 
        text = element_text(size=16),
        legend.position = 'none'
    )
p + geom_area(stat='identity')

Plotting 'true' taxon abundance distribution (from priming exp dataset)





In [690]:



    


%%R -i metaDataFile
# loading priming_exp metadata file

meta = read.delim(metaDataFile, sep='\t')
meta %>% head(n=4)



    


















    








            Sample FractionNum Bulk Control CC X100 X700 H2O Day Density rep
1 12C.000.28.03.07           7    0       1  1    0    0   0  28  1.7646    
2 12C.000.28.03.08           8    0       1  1    0    0   0  28  1.7614    
3 12C.000.28.03.09           9    0       1  1    0    0   0  28  1.7537    
4 12C.000.28.03.10          10    0       1  1    0    0   0  28  1.7483    
  contolVlabel Treatment
1      control    12C000
2      control    12C000
3      control    12C000
4      control    12C000


















In [691]:



    


%%R -i otuTableFile
# loading priming_exp OTU table 

tbl.otu.true = read.delim(otuTableFile, sep='\t') %>%
    select(OTUId, starts_with('X12C.700.14')) 
tbl.otu.true %>% head(n=3)



    


















    








     OTUId X12C.700.14.06.14 X12C.700.14.06.05 X12C.700.14.06.16
1 OTU.4776                34               142                11
2 OTU.2864                 1                16                 1
3 OTU.8170                 0                 0                 0
  X12C.700.14.06.11 X12C.700.14.06.13 X12C.700.14.06.09 X12C.700.14.06.04
1                18                30                27                97
2                 2                 0                 1                 3
3                 0                 0                 0                 0
  X12C.700.14.06.20 X12C.700.14.06.10 X12C.700.14.06.15 X12C.700.14.06.08
1               226                23                19                35
2                 1                 0                 1                 0
3                 0                 1                 0                 0
  X12C.700.14.06.12 X12C.700.14.06.18 X12C.700.14.06.17 X12C.700.14.06.19
1                25                61                27               136
2                 0                 2                 2                 0
3                 0                 0                 0                 0
  X12C.700.14.06.23 X12C.700.14.06.21 X12C.700.14.06.06 X12C.700.14.06.07
1                85               283                50                 0
2                 0                 1                 0                 0
3                 0                 0                 0                 0
  X12C.700.14.06.22 X12C.700.14.05.NA X12C.700.14.06.NA
1               208                51                26
2                 2                 0                 0
3                 0                 0                 0


















In [692]:



    


%%R
# editing table
tbl.otu.true.w = tbl.otu.true %>%
    gather('sample', 'count', 2:ncol(tbl.otu.true)) %>%
    mutate(sample = gsub('^X', '', sample)) %>%
    group_by(sample) %>%
    mutate(rel_abund = count / sum(count)) %>%
    ungroup() %>%
    filter(count > 0)
tbl.otu.true.w %>% head(n=5)



    


















    








Source: local data frame [5 x 4]

     OTUId           sample count    rel_abund
1 OTU.4776 12C.700.14.06.14    34 7.263716e-04
2 OTU.2864 12C.700.14.06.14     1 2.136387e-05
3 OTU.5406 12C.700.14.06.14     2 4.272774e-05
4 OTU.6001 12C.700.14.06.14     1 2.136387e-05
5  OTU.611 12C.700.14.06.14    23 4.913690e-04


















In [693]:



    


%%R
tbl.true.j = inner_join(tbl.otu.true.w, meta, c('sample' = 'Sample'))
tbl.true.j %>% as.data.frame %>% head(n=3)



    


















    








     OTUId           sample count    rel_abund FractionNum Bulk Control CC X100
1 OTU.4776 12C.700.14.06.14    34 7.263716e-04          14    0       1  0    0
2 OTU.2864 12C.700.14.06.14     1 2.136387e-05          14    0       1  0    0
3 OTU.5406 12C.700.14.06.14     2 4.272774e-05          14    0       1  0    0
  X700 H2O Day Density rep contolVlabel Treatment
1    1   0  14  1.7122          control    12C700
2    1   0  14  1.7122          control    12C700
3    1   0  14  1.7122          control    12C700


















In [694]:



    


%%R -w 800 -h 300
# plotting number of taxa at each BD

tbl.nt = tbl %>%
    filter(count > 0) %>%
    group_by(library, BD_mid) %>%
    summarize(n_taxa = n())

## plot
ggplot(tbl.nt, aes(BD_mid, n_taxa)) +
    geom_area(stat='identity', alpha=0.5) +
    geom_point() +
    geom_vline(xintercept=c(BD.GCp0, BD.GCp100), linetype='dashed', alpha=0.5) +
    labs(x='Buoyant density', y='Number of taxa') +
    theme_bw() +
    theme( 
        text = element_text(size=16),
        legend.position = 'none'
    )



    


















    
























In [695]:



    


%%R -w 700 -h 350

tbl.true.j.s = tbl.true.j %>%
    filter(count > 0) %>%
    group_by(sample, Density) %>%
    summarize(n_taxa = sum(count > 0))

ggplot(tbl.true.j.s, aes(Density, n_taxa)) +
    geom_area(stat='identity', alpha=0.5) +
    geom_point() +
    geom_vline(xintercept=c(BD.GCp0, BD.GCp100), linetype='dashed', alpha=0.5) +
    labs(x='Buoyant density', y='Number of taxa') +
    theme_bw() +
    theme( 
        text = element_text(size=16),
        legend.position = 'none'
    )

Plotting total counts for each sample





In [696]:



    


%%R -h 300 -w 600
tbl.true.j.s = tbl.true.j %>%
    group_by(sample, Density) %>%
    summarize(total_count = sum(count)) 

ggplot(tbl.true.j.s, aes(Density, total_count)) +
    geom_point() +
    geom_line() +
    labs(x='Buoyant density', y='Total sequences') +
    theme_bw() +
    theme(
        text = element_text(size=16)
        )

Plotting abundance distribution of target OTUs





In [697]:



    


%%R
tbl.true.j.f = tbl.true.j %>%
    filter(OTUId %in% targets) %>%
    arrange(OTUId, Density) %>%
    group_by(sample)
tbl.true.j.f %>% head(n=3) %>% as.data.frame



    


















    








  OTUId           sample count  rel_abund FractionNum Bulk Control CC X100 X700
1 OTU.1 12C.700.14.06.23   736 0.02455871          23    0       1  0    0    1
2 OTU.1 12C.700.14.06.22  1229 0.02870556          22    0       1  0    0    1
3 OTU.1 12C.700.14.06.21  1560 0.03320067          21    0       1  0    0    1
  H2O Day Density rep contolVlabel Treatment
1   0  14  1.6772          control    12C700
2   0  14  1.6805          control    12C700
3   0  14  1.6849          control    12C700


















In [698]:



    


%%R -w 800 -h 250
# plotting relative abundances

## plot
ggplot(tbl.true.j.f, aes(Density, rel_abund, fill=OTUId)) +
    geom_area(stat='identity') +
    geom_vline(xintercept=c(BD.GCp0, BD.GCp100), linetype='dashed', alpha=0.5) +
    labs(x='Buoyant density') +
    theme_bw() +
    theme( 
        text = element_text(size=16),
        legend.position = 'none'
    )

Combining true and simulated OTU tables for target taxa





In [699]:



    


%%R
tbl.f.e = tbl.f %>%
    mutate(library = 'simulation') %>%
    rename('density' = BD_mid) %>%
    select(-BD_min, -BD_max)

tbl.true.e = tbl.true.j.f %>% 
    select('taxon' = OTUId,
           'fraction' = sample,
           'density' = Density,
           count, rel_abund) %>%
    mutate(library = 'true') 
           
           
tbl.sim.true = rbind(tbl.f.e, tbl.true.e)
tbl.f.e = data.frame()
tbl.true.e = data.frame()

tbl.sim.true %>% head(n=3)



    


















    








Source: local data frame [3 x 6]
Groups: fraction

     library    fraction taxon density count    rel_abund
1 simulation  -inf-1.660 OTU.1   1.659    19 0.0013704559
2 simulation 1.660-1.664 OTU.1   1.662     4 0.0002569868
3 simulation 1.664-1.666 OTU.1   1.665     0 0.0000000000


















In [700]:



    


%%R
# check
cat('Number of target taxa: ', tbl.sim.true$taxon %>% unique %>% length, '\n')



    


















    








Number of target taxa:  108

Abundance distributions of each target taxon





In [701]:



    


%%R -w 900 -h 3000

tbl.sim.true = tbl.sim.true %>%
    ungroup() %>%
    group_by(taxon) %>%
    mutate(mean_rel_abund = mean(rel_abund)) %>%
    ungroup()

tbl.sim.true$taxon = reorder(tbl.sim.true$taxon, -tbl.sim.true$mean_rel_abund)

ggplot(tbl.sim.true, aes(density, rel_abund, color=library)) +
    geom_point() +
    geom_line() +
    theme_bw() +
    facet_wrap(~ taxon, ncol=4, scales='free_y')

Simulating an OTU table (10x more total abundance)





In [3]:



    


!cd $workDir; \
    SIPSim OTU_table \
    ampFrags_wRand_kde_dif_incorp.pkl \
    comm.txt \
    fracs.txt \
    --abs 1e10 \
    --np $nprocs \
    > OTU_abs1e10.txt



    


















    






Loading files...
Simulating OTUs...
Processing library: "1"
  Processing taxon: "OTU.22"
   taxon abs-abundance:  243100243
  Processing taxon: "OTU.43"
   taxon abs-abundance:  53386720
  Processing taxon: "OTU.81"
   taxon abs-abundance:  32890033
  Processing taxon: "OTU.116"
   taxon abs-abundance:  25263359
  Processing taxon: "OTU.17"
   taxon abs-abundance:  18590019
  Processing taxon: "OTU.66"
   taxon abs-abundance:  15730016
  Processing taxon: "OTU.8846"
   taxon abs-abundance:  13823347
  Processing taxon: "OTU.149"
   taxon abs-abundance:  10963344
  Processing taxon: "OTU.107"
   taxon abs-abundance:  10010010
  Processing taxon: "OTU.6861"
   taxon abs-abundance:  8103341
  Processing taxon: "OTU.470"
   taxon abs-abundance:  7150007
  Processing taxon: "OTU.3355"
   taxon abs-abundance:  6196673
  Processing taxon: "OTU.5691"
   taxon abs-abundance:  5720006
  Processing taxon: "OTU.294"
   taxon abs-abundance:  4766671
  Processing taxon: "OTU.436"
   taxon abs-abundance:  4290004
  Processing taxon: "OTU.725"
   taxon abs-abundance:  4290004
  Processing taxon: "OTU.356"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.3328"
   taxon abs-abundance:  3336670
  Processing taxon: "OTU.310"
   taxon abs-abundance:  3336670
  Processing taxon: "OTU.6013"
   taxon abs-abundance:  2860003
  Processing taxon: "OTU.7851"
   taxon abs-abundance:  3336670
  Processing taxon: "OTU.419"
   taxon abs-abundance:  4766671
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.276"
   taxon abs-abundance:  4766671
  Processing taxon: "OTU.4938"
   taxon abs-abundance:  6196673
  Processing taxon: "OTU.539"
   taxon abs-abundance:  4290004
  Processing taxon: "OTU.982"
   taxon abs-abundance:  2860003
  Processing taxon: "OTU.429"
   taxon abs-abundance:  8103341
  Processing taxon: "OTU.10167"
   taxon abs-abundance:  3336670
  Processing taxon: "OTU.213"
   taxon abs-abundance:  3336670
  Processing taxon: "OTU.317"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.326"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.428"
   taxon abs-abundance:  10010010
  Processing taxon: "OTU.7040"
   taxon abs-abundance:  5720006
  Processing taxon: "OTU.1583"
   taxon abs-abundance:  4766671
  Processing taxon: "OTU.421"
   taxon abs-abundance:  4290004
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.1712"
   taxon abs-abundance:  4290004
  Processing taxon: "OTU.6783"
   taxon abs-abundance:  3336670
  Processing taxon: "OTU.3156"
   taxon abs-abundance:  7150007
  Processing taxon: "OTU.616"
   taxon abs-abundance:  13346680
  Processing taxon: "OTU.1417"
   taxon abs-abundance:  2860003
  Processing taxon: "OTU.194"
   taxon abs-abundance:  10963344
  Processing taxon: "OTU.505"
   taxon abs-abundance:  3336670
  Processing taxon: "OTU.121"
   taxon abs-abundance:  15730016
  Processing taxon: "OTU.329"
   taxon abs-abundance:  4766671
  Processing taxon: "OTU.747"
   taxon abs-abundance:  4290004
  Processing taxon: "OTU.6616"
   taxon abs-abundance:  3336670
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.402"
   taxon abs-abundance:  3336670
  Processing taxon: "OTU.201"
   taxon abs-abundance:  5720006
  Processing taxon: "OTU.5683"
   taxon abs-abundance:  8103341
  Processing taxon: "OTU.726"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.478"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.399"
   taxon abs-abundance:  6196673
  Processing taxon: "OTU.1830"
   taxon abs-abundance:  3336670
  Processing taxon: "OTU.666"
   taxon abs-abundance:  2860003
  Processing taxon: "OTU.204"
   taxon abs-abundance:  4290004
  Processing taxon: "OTU.543"
   taxon abs-abundance:  4766671
  Processing taxon: "OTU.409"
   taxon abs-abundance:  18590019
  Processing taxon: "OTU.384"
   taxon abs-abundance:  3336670
  Processing taxon: "OTU.11322"
   taxon abs-abundance:  5720006
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.542"
   taxon abs-abundance:  5720006
  Processing taxon: "OTU.111"
   taxon abs-abundance:  3336670
  Processing taxon: "OTU.4245"
   taxon abs-abundance:  2860003
  Processing taxon: "OTU.2256"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.8111"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.161"
   taxon abs-abundance:  8103341
  Processing taxon: "OTU.3190"
   taxon abs-abundance:  7150007
  Processing taxon: "OTU.6358"
   taxon abs-abundance:  9533343
  Processing taxon: "OTU.340"
   taxon abs-abundance:  4290004
  Processing taxon: "OTU.867"
   taxon abs-abundance:  4766671
  Processing taxon: "OTU.5875"
   taxon abs-abundance:  3336670
  Processing taxon: "OTU.162"
   taxon abs-abundance:  10963344
  Processing taxon: "OTU.100"
   taxon abs-abundance:  13346680
  Processing taxon: "OTU.155"
   taxon abs-abundance:  5720006
  Processing taxon: "OTU.9449"
   taxon abs-abundance:  3336670
  Processing taxon: "OTU.6407"
  Processing taxon: "OTU.180"
   taxon abs-abundance:  6196673
   taxon abs-abundance:  2860003
  Processing taxon: "OTU.7381"
   taxon abs-abundance:  4766671
  Processing taxon: "OTU.592"
   taxon abs-abundance:  3336670
  Processing taxon: "OTU.642"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.351"
   taxon abs-abundance:  4290004
  Processing taxon: "OTU.4204"
   taxon abs-abundance:  15253349
  Processing taxon: "OTU.604"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.5587"
   taxon abs-abundance:  7150007
  Processing taxon: "OTU.484"
   taxon abs-abundance:  8103341
  Processing taxon: "OTU.4038"
   taxon abs-abundance:  3336670
  Processing taxon: "OTU.280"
   taxon abs-abundance:  5243339
  Processing taxon: "OTU.535"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.12027"
   taxon abs-abundance:  9533343
  Processing taxon: "OTU.288"
   taxon abs-abundance:  4766671
  Processing taxon: "OTU.1908"
   taxon abs-abundance:  3336670
  Processing taxon: "OTU.6966"
   taxon abs-abundance:  2860003
  Processing taxon: "OTU.843"
   taxon abs-abundance:  3336670
  Processing taxon: "OTU.1098"
   taxon abs-abundance:  3336670
  Processing taxon: "OTU.235"
   taxon abs-abundance:  4290004
  Processing taxon: "OTU.7536"
   taxon abs-abundance:  25263359
  Processing taxon: "OTU.10129"
   taxon abs-abundance:  6196673
  Processing taxon: "OTU.647"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.6983"
   taxon abs-abundance:  4766671
  Processing taxon: "OTU.11478"
   taxon abs-abundance:  13346680
  Processing taxon: "OTU.127"
   taxon abs-abundance:  10963344
  Processing taxon: "OTU.5118"
   taxon abs-abundance:  2860003
  Processing taxon: "OTU.8432"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.42"
   taxon abs-abundance:  18113351
  Processing taxon: "OTU.6450"
   taxon abs-abundance:  8103341
  Processing taxon: "OTU.1638"
   taxon abs-abundance:  3336670
  Processing taxon: "OTU.8842"
   taxon abs-abundance:  5243339
  Processing taxon: "OTU.264"
   taxon abs-abundance:  7150007
  Processing taxon: "OTU.2158"
   taxon abs-abundance:  2860003
  Processing taxon: "OTU.24"
   taxon abs-abundance:  32890033
  Processing taxon: "OTU.177"
   taxon abs-abundance:  4766671
  Processing taxon: "OTU.744"
   taxon abs-abundance:  3336670
  Processing taxon: "OTU.1058"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.314"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.275"
   taxon abs-abundance:  6196673
  Processing taxon: "OTU.286"
   taxon abs-abundance:  2860003
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.6962"
   taxon abs-abundance:  2860003
  Processing taxon: "OTU.6217"
   taxon abs-abundance:  15253349
  Processing taxon: "OTU.3922"
   taxon abs-abundance:  3336670
  Processing taxon: "OTU.256"
   taxon abs-abundance:  4290004
  Processing taxon: "OTU.576"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.9399"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.203"
   taxon abs-abundance:  2860003
  Processing taxon: "OTU.420"
   taxon abs-abundance:  8103341
  Processing taxon: "OTU.273"
   taxon abs-abundance:  4766671
  Processing taxon: "OTU.258"
   taxon abs-abundance:  7150007
  Processing taxon: "OTU.179"
   taxon abs-abundance:  9533343
  Processing taxon: "OTU.847"
   taxon abs-abundance:  5243339
  Processing taxon: "OTU.463"
   taxon abs-abundance:  3336670
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.658"
   taxon abs-abundance:  3336670
  Processing taxon: "OTU.6439"
   taxon abs-abundance:  6196673
  Processing taxon: "OTU.4922"
   taxon abs-abundance:  10963344
  Processing taxon: "OTU.5642"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.498"
   taxon abs-abundance:  3336670
  Processing taxon: "OTU.1981"
   taxon abs-abundance:  2860003
  Processing taxon: "OTU.327"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.109"
   taxon abs-abundance:  4766671
  Processing taxon: "OTU.51"
   taxon abs-abundance:  4290004
  Processing taxon: "OTU.341"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.214"
   taxon abs-abundance:  7150007
  Processing taxon: "OTU.646"
   taxon abs-abundance:  6196673
  Processing taxon: "OTU.185"
   taxon abs-abundance:  8103341
  Processing taxon: "OTU.369"
   taxon abs-abundance:  3336670
  Processing taxon: "OTU.320"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.3477"
   taxon abs-abundance:  3336670
  Processing taxon: "OTU.13701"
   taxon abs-abundance:  4766671
  Processing taxon: "OTU.210"
   taxon abs-abundance:  2860003
  Processing taxon: "OTU.7789"
   taxon abs-abundance:  18113351
  Processing taxon: "OTU.293"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.191"
   taxon abs-abundance:  5243339
  Processing taxon: "OTU.73"
   taxon abs-abundance:  13346680
  Processing taxon: "OTU.225"
   taxon abs-abundance:  3336670
  Processing taxon: "OTU.2944"
   taxon abs-abundance:  4290004
  Processing taxon: "OTU.360"
   taxon abs-abundance:  10486677
  Processing taxon: "OTU.589"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.5262"
   taxon abs-abundance:  6196673
  Processing taxon: "OTU.236"
   taxon abs-abundance:  4766671
  Processing taxon: "OTU.150"
   taxon abs-abundance:  3336670
  Processing taxon: "OTU.212"
   taxon abs-abundance:  2860003
  Processing taxon: "OTU.4278"
   taxon abs-abundance:  7150007
  Processing taxon: "OTU.145"
   taxon abs-abundance:  3336670
  Processing taxon: "OTU.13773"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.5575"
   taxon abs-abundance:  8103341
  Processing taxon: "OTU.3342"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.57"
   taxon abs-abundance:  24786691
  Processing taxon: "OTU.597"
   taxon abs-abundance:  3336670
  Processing taxon: "OTU.464"
   taxon abs-abundance:  4766671
  Processing taxon: "OTU.1528"
   taxon abs-abundance:  9533343
  Processing taxon: "OTU.3886"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.171"
   taxon abs-abundance:  6196673
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.2584"
   taxon abs-abundance:  6196673
  Processing taxon: "OTU.300"
   taxon abs-abundance:  2860003
  Processing taxon: "OTU.5724"
   taxon abs-abundance:  3336670
  Processing taxon: "OTU.198"
   taxon abs-abundance:  5243339
  Processing taxon: "OTU.263"
   taxon abs-abundance:  4290004
  Processing taxon: "OTU.190"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.4933"
   taxon abs-abundance:  3336670
  Processing taxon: "OTU.4133"
   taxon abs-abundance:  6673340
  Processing taxon: "OTU.8359"
   taxon abs-abundance:  10486677
  Processing taxon: "OTU.3287"
   taxon abs-abundance:  4766671
  Processing taxon: "OTU.99"
   taxon abs-abundance:  15253349
  Processing taxon: "OTU.372"
   taxon abs-abundance:  8103341
  Processing taxon: "OTU.3388"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.4450"
   taxon abs-abundance:  2860003
  Processing taxon: "OTU.253"
   taxon abs-abundance:  6196673
  Processing taxon: "OTU.395"
   taxon abs-abundance:  2860003
  Processing taxon: "OTU.5763"
   taxon abs-abundance:  3336670
  Processing taxon: "OTU.398"
   taxon abs-abundance:  2860003
  Processing taxon: "OTU.238"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.740"
   taxon abs-abundance:  4766671
  Processing taxon: "OTU.217"
   taxon abs-abundance:  6673340
  Processing taxon: "OTU.5374"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.265"
   taxon abs-abundance:  4290004
  Processing taxon: "OTU.468"
   taxon abs-abundance:  2860003
  Processing taxon: "OTU.84"
   taxon abs-abundance:  31936699
  Processing taxon: "OTU.328"
   taxon abs-abundance:  5243339
  Processing taxon: "OTU.345"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.495"
   taxon abs-abundance:  2860003
  Processing taxon: "OTU.227"
   taxon abs-abundance:  6196673
  Processing taxon: "OTU.173"
   taxon abs-abundance:  8103341
  Processing taxon: "OTU.801"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.7773"
   taxon abs-abundance:  4766671
  Processing taxon: "OTU.442"
   taxon abs-abundance:  2860003
  Processing taxon: "OTU.842"
   taxon abs-abundance:  3336670
  Processing taxon: "OTU.61"
   taxon abs-abundance:  13346680
  Processing taxon: "OTU.3380"
   taxon abs-abundance:  10486677
  Processing taxon: "OTU.11207"
   taxon abs-abundance:  6673340
  Processing taxon: "OTU.114"
   taxon abs-abundance:  2860003
  Processing taxon: "OTU.6201"
   taxon abs-abundance:  3813337
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.335"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.1045"
   taxon abs-abundance:  2860003
  Processing taxon: "OTU.771"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.7088"
   taxon abs-abundance:  9533343
  Processing taxon: "OTU.3406"
   taxon abs-abundance:  4766671
  Processing taxon: "OTU.4434"
   taxon abs-abundance:  18113351
  Processing taxon: "OTU.322"
   taxon abs-abundance:  4290004
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.7337"
   taxon abs-abundance:  4290004
  Processing taxon: "OTU.688"
   taxon abs-abundance:  2860003
  Processing taxon: "OTU.593"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.305"
   taxon abs-abundance:  2860003
  Processing taxon: "OTU.559"
   taxon abs-abundance:  6196673
  Processing taxon: "OTU.350"
   taxon abs-abundance:  3336670
  Processing taxon: "OTU.101"
   taxon abs-abundance:  7626674
  Processing taxon: "OTU.298"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.166"
   taxon abs-abundance:  5243339
  Processing taxon: "OTU.246"
   taxon abs-abundance:  6673340
  Processing taxon: "OTU.3817"
   taxon abs-abundance:  2860003
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.270"
   taxon abs-abundance:  2860003
  Processing taxon: "OTU.502"
   taxon abs-abundance:  4766671
  Processing taxon: "OTU.38"
   taxon abs-abundance:  14776681
  Processing taxon: "OTU.330"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.503"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.7237"
   taxon abs-abundance:  2860003
  Processing taxon: "OTU.364"
   taxon abs-abundance:  3336670
  Processing taxon: "OTU.5866"
   taxon abs-abundance:  2860003
  Processing taxon: "OTU.4351"
   taxon abs-abundance:  4290004
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.462"
   taxon abs-abundance:  4290004
  Processing taxon: "OTU.11076"
   taxon abs-abundance:  4766671
  Processing taxon: "OTU.307"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.853"
   taxon abs-abundance:  2860003
  Processing taxon: "OTU.183"
   taxon abs-abundance:  7626674
  Processing taxon: "OTU.460"
   taxon abs-abundance:  6673340
  Processing taxon: "OTU.334"
   taxon abs-abundance:  3336670
  Processing taxon: "OTU.45"
   taxon abs-abundance:  13346680
  Processing taxon: "OTU.1856"
   taxon abs-abundance:  9056676
  Processing taxon: "OTU.63"
   taxon abs-abundance:  51003384
  Processing taxon: "OTU.7056"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.418"
   taxon abs-abundance:  2860003
  Processing taxon: "OTU.7827"
   taxon abs-abundance:  3336670
  Processing taxon: "OTU.257"
   taxon abs-abundance:  5243339
  Processing taxon: "OTU.1105"
   taxon abs-abundance:  2860003
  Processing taxon: "OTU.279"
   taxon abs-abundance:  3813337
  Processing taxon: "OTU.157"
   taxon abs-abundance:  6196673
  Processing taxon: "OTU.5611"
   taxon abs-abundance:  4766671
  Processing taxon: "OTU.4776"
   taxon abs-abundance:  24310024
  Processing taxon: "OTU.251"
   taxon abs-abundance:  3336670
  Processing taxon: "OTU.2845"
   taxon abs-abundance:  6673340
  Processing taxon: "OTU.457"
   taxon abs-abundance:  4290004
  Processing taxon: "OTU.206"
   taxon abs-abundance:  7626674
  Processing taxon: "OTU.75"
   taxon abs-abundance:  10486677
  Processing taxon: "OTU.244"
   taxon abs-abundance:  2860003
  Processing taxon: "OTU.1628"
   taxon abs-abundance:  4766671
  Processing taxon: "OTU.1954"
   taxon abs-abundance:  2860003
  Processing taxon: "OTU.156"
   taxon abs-abundance:  14776681
  Processing taxon: "OTU.422"
   taxon abs-abundance:  3336670
  Processing taxon: "OTU.158"
   taxon abs-abundance:  9056676
  Processing taxon: "OTU.5367"
   taxon abs-abundance:  3813337
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   WARNING: No bins for taxon; likely caused by no BD KDE
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   WARNING: No bins for taxon; likely caused by no BD KDE
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   WARNING: No bins for taxon; likely caused by no BD KDE
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  Processing taxon: "OTU.7805"
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In [18]:



    


%%R -i workDir
setwd(workDir)

# loading file
tbl = read.delim('OTU_abs1e10.txt', sep='\t')



    











In [19]:



    


%%R
## BD for G+C of 0 or 100
BD.GCp0 = 0 * 0.098 + 1.66
BD.GCp100 = 1 * 0.098 + 1.66



    











In [20]:



    


%%R -w 800 -h 300
# plotting absolute abundances

tbl.s = tbl %>%
    group_by(library, BD_mid) %>%
    summarize(total_count = sum(count))

## plot
p = ggplot(tbl.s, aes(BD_mid, total_count)) +
    geom_area(stat='identity', alpha=0.3, position='dodge') +
    geom_histogram(stat='identity') +
    geom_vline(xintercept=c(BD.GCp0, BD.GCp100), linetype='dashed', alpha=0.5) +
    labs(x='Buoyant density') +
    theme_bw() +
    theme( 
        text = element_text(size=16) 
    )
p



    


















    
























In [21]:



    


%%R -w 800 -h 300
# plotting number of taxa at each BD

tbl.nt = tbl %>%
    filter(count > 0) %>%
    group_by(library, BD_mid) %>%
    summarize(n_taxa = n())

## plot
p = ggplot(tbl.nt, aes(BD_mid, n_taxa)) +
    geom_area(stat='identity', alpha=0.3, position='dodge') +
    geom_histogram(stat='identity') +
    geom_vline(xintercept=c(BD.GCp0, BD.GCp100), linetype='dashed', alpha=0.5) +
    labs(x='Buoyant density', y='Number of taxa') +
    theme_bw() +
    theme( 
        text = element_text(size=16),
        legend.position = 'none'
    )
p

Notes:

  • Veil line lowered a bit, but nothing substantial, especially for a 10x increase in sampling depth.

Subsampling from the OTU table





In [78]:



    


dist,loc,scale = seq_per_fraction

!cd $workDir; \
    SIPSim OTU_subsample \
    --dist $dist \
    --dist_params mean:$loc,sigma:$scale \
    --min_size 10000 \
    --max_size 200000 \
    --walk 2 \
    OTU_abs1e10.txt \
    > OTU_abs1e10_sub.txt



    











In [79]:



    


# debug
# !cd $workDir; \
#     SIPSim OTU_subsample \
#     --dist uniform \
#     --dist_params low:100000000,high:100000000 \
#     OTU_abs1e10.txt \
#     > OTU_abs1e10_sub.txt

Plotting the distribution of sample sizes





In [80]:



    


%%R -h 300
setwd(workDir)

tbl = read.csv('OTU_abs1e10_sub.txt', sep='\t') 

tbl.s = tbl %>% 
    group_by(library, fraction) %>%
    summarize(total_count = sum(count)) %>%
    ungroup() %>%
    mutate(library = as.character(library))

ggplot(tbl.s, aes(total_count)) +
    geom_density(fill='blue')



    


















    
























In [81]:



    


%%R -h 300 -w 800
setwd(workDir)

tbl.s = tbl %>%
    group_by(fraction, BD_min, BD_mid, BD_max) %>%
    summarize(total_count = sum(count)) 

ggplot(tbl.s, aes(BD_mid, total_count)) +
    geom_point() +
    geom_line() +
    labs(x='Buoyant density', y='Total sequences') +
    theme_bw() +
    theme(
        text = element_text(size=16)
        )



    


















    
























In [82]:



    


%%R -w 800 -h 300
# plotting number of taxa at each BD

tbl.nt = tbl %>%
    filter(count > 0) %>%
    group_by(library, fraction, BD_mid) %>%
    summarize(n_taxa = n())

## plot
ggplot(tbl.nt, aes(BD_mid, n_taxa)) +
    geom_area(stat='identity', alpha=0.5) +
    geom_point() +
    geom_vline(xintercept=c(BD.GCp0, BD.GCp100), linetype='dashed', alpha=0.5) +
    labs(x='Buoyant density', y='Number of taxa') +
    theme_bw() +
    theme( 
        text = element_text(size=16),
        legend.position = 'none'
    )

debug: Ploitting OTU counts for densities with lower number of taxa





In [72]:



    


%%R -i workDir
setwd(workDir)

# loading file
tbl = read.delim('OTU_abs1e10.txt', sep='\t')



    











In [73]:



    


%%R -w 800
tbl.1.737 = tbl %>%
    filter(BD_mid == 1.737) %>%
    mutate(rank = row_number(-count))

ggplot(tbl.1.737, aes(rank, count)) +
    geom_point() +
    scale_y_log10()



    


















    
























In [74]:



    


%%R
tbl.1.737 %>%
    filter(count > 0) %>%
    group_by(library) %>% 
    mutate(total_abund = sum(count)) %>%
    ungroup() %>%
    mutate(rel_abund = count / total_abund) %>%
    arrange(rel_abund) %>%
    as.data.frame() %>%
    head



    


















    








  library     taxon    fraction BD_min BD_mid BD_max count rank total_abund
1       1   OTU.109 1.734-1.740  1.734  1.737   1.74     1 1937   162835186
2       1  OTU.1117 1.734-1.740  1.734  1.737   1.74     1 1938   162835186
3       1 OTU.12311 1.734-1.740  1.734  1.737   1.74     1 1939   162835186
4       1  OTU.1813 1.734-1.740  1.734  1.737   1.74     1 1940   162835186
5       1  OTU.2019 1.734-1.740  1.734  1.737   1.74     1 1941   162835186
6       1   OTU.219 1.734-1.740  1.734  1.737   1.74     1 1942   162835186
     rel_abund
1 6.141179e-09
2 6.141179e-09
3 6.141179e-09
4 6.141179e-09
5 6.141179e-09
6 6.141179e-09


















In [ ]:

Content source: nick-youngblut/SIPSim

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