Description:

Example buoyant density distributions for 4 bacteria taxa

Making histograms of example taxa used for 16S region GC conservation figure

  "Clostridium ljungdahlii DSM 13528",
  "Escherichia coli APEC O78",
  "Streptomyces griseus subsp griseus\nNBRC 13350",
  "Lactobacillus gasseri ATCC 33323"

Plotting GC content for amplicons & shotgun reads

parsing out just taxa of interest from read GC files

amplicons

@ system76-server:~/notebook/deltaGC_notes/data/amplicon/140411_allBac/amp454-L215-N1k/140425_example-taxa

made a file of all 4 taxa
- taxa_list.txt
  
  $ head -n 1 ../skewnorm_m10k_r4k-11.5k.txt > skewnorm_m10k_r4k-11.5k_exp.txt; grep -f taxa_list.txt ../skewnorm_m10k_r4k-11.5k.txt >> skewnorm_m10k_r4k-11.5k_exp.txt
  
  $ head -n 1 ../skewnorm_m15k_r4k-20k.txt > skewnorm_m15k_r4k-20k_exp.txt; grep -f taxa_list.txt ../skewnorm_m15k_r4k-20k.txt >> skewnorm_m15k_r4k-20k_exp.txt

metagenomes

@ system76-server:~/notebook/deltaGC_notes/data/mg-reads/140411_allBac/mg454-L215-N10k/140425_example-taxa

$ cp ~/notebook/deltaGC_notes/data/amplicon/140411_allBac/amp454-L215-N1k/140425_example-taxa/taxa_list.txt .

$ head -n 1 ../skewnorm_m10k_r4k-11.5k.txt > skewnorm_m10k_r4k-11.5k_exp.txt; grep -f taxa_list.txt ../skewnorm_m10k_r4k-11.5k.txt >> skewnorm_m10k_r4k-11.5k_exp.txt

$ head -n 1 ../skewnorm_m15k_r4k-20k.txt > skewnorm_m15k_r4k-20k_exp.txt; grep -f taxa_list.txt ../skewnorm_m15k_r4k-20k.txt >> skewnorm_m15k_r4k-20k_exp.txt



In [1]:

    
%load_ext rmagic
%load_ext rpy2.ipython









    



/opt/anaconda/lib/python2.7/site-packages/pytz/__init__.py:29: UserWarning: Module argparse was already imported from /opt/anaconda/lib/python2.7/argparse.pyc, but /opt/anaconda/lib/python2.7/site-packages is being added to sys.path
  from pkg_resources import resource_stream



In [2]:

    
%%R
# loading tables
require(ggplot2)
require(data.table)
require(gridExtra)









    





Loading required package: ggplot2
Loading required package: data.table
data.table 1.9.2  For help type: help("data.table")
Loading required package: gridExtra
Loading required package: grid

Loading amplicon deltaGC data



In [3]:

    
%%R
base.dir = "~/notebook/deltaGC_notes/data/amplicon/140411_allBac/amp454-L215-N1k/140425_example-taxa";
files = c(
    'skewnorm_m15k_r4k-20k_exp',
    'skewnorm_m10k_r4k-11.5k_exp'
    )

tbl.l = list()
for(i in files){
    in.file = paste(c(i, "txt"), collapse=".")
    in.file = paste(c(base.dir, in.file), collapse="/")
    tbl.l[[i]] = fread(in.file, header=T, sep="\t")
    tbl.l[[i]]$file = rep(i, nrow(tbl.l[[i]]))
    }

tbl.amp = do.call(rbind, tbl.l)

Loading shotgun read deltaGC data



In [4]:

    
%%R
base.dir = "~/notebook/deltaGC_notes/data/mg-reads/140411_allBac/mg454-L215-N10k/140425_example-taxa/";
files = list(
    'skewnorm_m15k_r4k-20k_exp',
    'skewnorm_m10k_r4k-11.5k_exp'
    )

tbl.l = list()
for(i in files){
    in.file = paste(c(i, "txt"), collapse=".")
    in.file = paste(c(base.dir, in.file), collapse="/")
    tbl.l[[i]] = fread(in.file, header=T, sep="\t")
    tbl.l[[i]]$file = rep(i, nrow(tbl.l[[i]]))
    }

tbl.mg = do.call(rbind, tbl.l)

Merging tables



In [5]:

    
%%R
# merging tables
tbl.amp[, dataset:= 'amplicon']
tbl.mg[, dataset:= 'shotgun']
tbl = rbind(tbl.amp, tbl.mg)

# editting values for plotting
tbl[, file:= gsub(".+m15k.+", "12.5 kb", file)]
tbl[, file:= gsub(".+m10k.+", "6 kb", file)]

## editing names
examples = c(
"Clostridium_ljungdahlii_DSM_13528",
"Escherichia_coli_APEC_O78",
"Streptomyces_griseus_subsp_griseus_NBRC_13350",  
"Lactobacillus_gasseri_ATCC_33323"
)
new.names = c(
"C. ljungdahlii",
"E. coli",
"S. griseus",
"L. gasseri"
)
for(i in 1:length(examples)){
    tbl$genome = gsub(examples[i], new.names[i], tbl$genome)
    }

# ordering of taxa
tbl$genome = factor(tbl$genome, levels=new.names)

# renaming 'dataset' to 'Fragments'
tbl[, Fragments := dataset]
tbl[, dataset := NULL]









    





           genome scaffold           read  read_GC read_buoyant_density
    1: L. gasseri CP000413  CP000413__418 52.55814             1.711507
    2: L. gasseri CP000413  CP000413__419 52.55814             1.711507
    3: L. gasseri CP000413  CP000413__412 52.55814             1.711507
    4: L. gasseri CP000413  CP000413__413 50.69767             1.709684
    5: L. gasseri CP000413  CP000413__410 50.69767             1.709684
   ---                                                                 
87996: S. griseus AP009493 AP009493__2047 60.46512             1.719256
87997: S. griseus AP009493 AP009493__2040 67.90698             1.726549
87998: S. griseus AP009493 AP009493__2041 70.23256             1.728828
87999: S. griseus AP009493 AP009493__2042 74.88372             1.733386
88000: S. griseus AP009493 AP009493__2043 79.06977             1.737488
       read_start read_length fragment_GC fragment_buoyant_density
    1:    3119592         215    49.50342                 1.708513
    2:    3585673         215    44.56862                 1.703677
    3:    3119592         215    46.30809                 1.705382
    4:     956257         215    44.01671                 1.703136
    5:    3132922         215    45.14824                 1.704245
   ---                                                            
87996:   15593419         215    73.57766                 1.732106
87997:   13676810         215    72.12288                 1.730680
87998:   15347106         215    70.99312                 1.729573
87999:   14283447         215    75.82455                 1.734308
88000:   10458701         215    75.74225                 1.734227
       fragment_start fragment_length    file Fragments
    1:        3119429           12284 12.5 kb  amplicon
    2:        3579137           14048 12.5 kb  amplicon
    3:        3108785           14911 12.5 kb  amplicon
    4:         951661           10053 12.5 kb  amplicon
    5:        3126169           12109 12.5 kb  amplicon
   ---                                                 
87996:       15591128            5730    6 kb   shotgun
87997:       13675673            6543    6 kb   shotgun
87998:       15345649            6102    6 kb   shotgun
87999:       14282870            5882    6 kb   shotgun
88000:       10455814            6130    6 kb   shotgun

Adding whole genome G+C content



In [6]:

    
%%R

# loading in genome GC table
tbl.genGC = fread("~/notebook/deltaGC_notes/data/genome_data/prok-bac-genomes_Ngaps_GC/prok-bac-genomes_Ngaps_GC.txt",
                    header=F)
## editing table
colnames(tbl.genGC) = c('genome', 'genome_GC')
tbl.genGC[,genome:=gsub(".+\\/|\\.fasta", "", genome)]

## selecting taxa of interest
examples = c(
"Clostridium_ljungdahlii_DSM_13528",
"Escherichia_coli_APEC_O78",
"Streptomyces_griseus_subsp_griseus_NBRC_13350",  
"Lactobacillus_gasseri_ATCC_33323"
)

tbl.genGC = subset(tbl.genGC, genome %in% examples)


## changing names
new.names = c(
"C. ljungdahlii",
"E. coli",
"S. griseus",
"L. gasseri"
)

for(i in 1:length(examples)){
    tbl.genGC$genome = gsub(examples[i], new.names[i], tbl.genGC$genome)
}


## calculating BD for each
tbl.genGC[, BD:= 0.098 * genome_GC + 1.66]









    





           genome genome_GC       BD
1:     S. griseus 0.7222741 1.730783
2:        E. coli 0.5068013 1.709667
3: C. ljungdahlii 0.3059600 1.689984
4:     L. gasseri 0.3468158 1.693988



In [21]:

    
%%R -w 7 -h 6 -u in
## plotting with mean GC
tbl1 = subset( tbl , file='12.5 kb' )

# plotting
p = ggplot(tbl1, aes(fragment_buoyant_density, fill=Fragments)) + 
        geom_density(alpha=0.5, size=0.4) +
        scale_fill_manual(values=c('blue', 'orange')) +
        facet_grid(genome ~ .) +
        geom_vline(data=tbl.genGC, aes(xintercept=BD), linetype='dashed') +
        labs(x=expression(paste("Fragment buoyant density (g ", ml^-1, ")")), 
             y="Kernel density") +
        theme( 
            text = element_text(size=18),
            axis.title.y = element_text(vjust=1),
            axis.title.x = element_text(vjust=0),
            axis.text.x = element_text(color='black'),
            axis.text.y = element_text(color='black'),           
            strip.text = element_text(face='italic'),
            strip.background = element_rect(size=4)
            )
ggsave("~/notebook/deltaGC_notes/data/amp-mg/figures/BD-dist_example-bac.tiff", 
          width=7, height=6, units='in', dpi=300)
print(p)
xxx=1