Game of Transposons: The Bells

## `summarise()` has grouped output by 'Condition', 'Day', 'Organism'. You can
## override using the `.groups` argument.
## `summarise()` has grouped output by 'Condition', 'Day'. You can override using
## the `.groups` argument.
## `summarise()` has grouped output by 'Condition', 'Day', 'Organism'. You can
## override using the `.groups` argument.
## `summarise()` has grouped output by 'Condition', 'Day'. You can override using
## the `.groups` argument.
## `summarise()` has grouped output by 'Condition', 'Day'. You can override using
## the `.groups` argument.

## `summarise()` has grouped output by 'Condition'. You can override using the
## `.groups` argument.

Total bacteria and diatoms were enumerated using flow cytometry (cells/ml; dotted line samples), while individual bacterial taxa were enumerated by CFU. Standard error of the mean is displayed for each treatment as black bars (n=4 for flow cytometry)

##Growth Curve

Expansion Factors

## [1] "RpomAlone Expansion="        "38.1"                       
## [3] "Vibrio Expansion="           "59.68"                      
## [5] "Marivivens Expansion="       "90.86"                      
## [7] "CompleteCommunity Expansion" "65.27"

Number of generations over 4 days

## [1] 0.132841

##      [,1]                             [,2]    [,3]   
## [1,] "rpomAlone Generations"          "6.362" "0.133"
## [2,] "Vibrio rpom Generations"        "5.381" "0.117"
## [3,] "Marivivens rpom Generations"    "5.783" "0.057"
## [4,] "Complete Comm rpom Generations" "4.438" "0.091"

## [1] "Mean Generations= 5.491"

Fitness analysis

Overview of fitness profiles

## [[1]]
## [1] "rpomAlone against vibrio spearman:"
## 
## $p.value
## [1] 0
## 
## $estimate
##       rho 
## 0.6371916

## [[1]]
## [1] "rpomAlone against marivivens spearman:"
## 
## $p.value
## [1] 0
## 
## $estimate
##       rho 
## 0.6887833

## [[1]]
## [1] "rpomAlone against Complete Commuinity spearman:"
## 
## $p.value
## [1] 0
## 
## $estimate
##       rho 
## 0.6269624

Testing the fitness increases and decreases

Ammonium/Nitrate growth curves

## `summarise()` has grouped output by 'Time', 'Organism'. You can override using
## the `.groups` argument.

Growth on glycolate

## `summarise()` has grouped output by 'Time', 'Organism'. You can override using
## the `.groups` argument.

## `summarise()` has grouped output by 'Time', 'Organism'. You can override using
## the `.groups` argument.

## `summarise()` has grouped output by 'Time', 'Organism'. You can override using
## the `.groups` argument.

## `summarise()` has grouped output by 'Time', 'Organism'. You can override using
## the `.groups` argument.

## `summarise()` has grouped output by 'Time', 'Organism'. You can override using
## the `.groups` argument.

aspartate <- fread('Data/DSS3,HF1,HF70_aspartate_48-well.csv') %>% 
    pivot_longer(., cols=-1, names_to='Organism', values_to='OD') %>% 
    na.omit() %>% 
    separate(., col='Organism', into=c('Organism', 'Condition', 'Rep')) %>% 
    group_by(Time, Organism, Condition) %>% 
    summarize(mean_OD=mean(OD), sem_OD=sd(OD)/sqrt(length(OD)))

## `summarise()` has grouped output by 'Time', 'Organism'. You can override using
## the `.groups` argument.

attach(aspartate)
rpomAspartate <- Organism=='DSS3' & Condition=='aspartate'
mariAspartate <- Organism=='HF1' & Condition=='aspartate'
vibAspartate <- Organism=='HF70' & Condition=='aspartate'
#pdf('aspartate.pdf')
plot(Time[rpomAsparagine], mean_OD[rpomAsparagine], type='n',  las=1, xlab='Time(h)', ylab='OD600', main='Aspartate', bty='n', ylim=c(0, 0.6),xlim=c(0, 20), cex=1.5, col='gray80')
OD(rpomAsparagine, rpomColor)
OD(vibAsparagine, vibColor)
OD(mariAsparagine, mariColor)

#dev.off()
detach(aspartate)

Cross feeding data

## `summarise()` has grouped output by 'Time', 'Strain'. You can override using
## the `.groups` argument.