/
run_everything.R
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run_everything.R
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source("exp012depletion_sankey.R")
source("exp2depletion.R")
source("exp3metabolomics.R")
source("exp3proteomics.R")
source("exp4spentmedia_metabolomics.R")
source("exp5concentration.R")
source("exp6transfers.R")
source("exp10bioaccumulation.R")
source("exp12nmr.R")
source("exp7spentmedia_Erectale_growth.R")
source("summary.R")
source("screen_vs_assay.R")
source("chemical_diversity.R")
# Create docker container
create.dockerfile = function()
{
library(containerit)
dfile = containerit::dockerfile(
copy="script_dir",
cmd=containerit::Cmd(params="run_everything.R"),
entrypoint=containerit::Entrypoint("Rscript", params=list("run_everything.R")),
versioned_packages=T)
write(dfile, file=file.path(getwd(), "Dockerfile"))
system("docker build --file Dockerfile --tag sandrejev/drugs_bioaccumulation .", wait=T)
system("docker save -o drugs_bioaccumulation.tar sandrejev/drugs_bioaccumulation:latest .", wait=T)
system("docker push sandrejev/drugs_bioaccumulation", wait=T)
}
exp012depletion.sankey() # Done (Figure 1)
exp12nmr_analyze() # Figure 2b
exp10bioaccumulation.analyze() # Figure 2c
exp6transfers.analyze() # Figure 3a
exp5concentration.analyze() # Figure 3b
exp7spentmedia.Erectale_growth() # Figure 3c
exp2depletion.total2supernatant()
exp3metabolomics.analyze()
exp3proteomics.analyze()
exp4spentmedia.metabolomics()
exp5concentration.analyze()
exp6transfers.analyze()
summary.bugs_piechart()
summary.enzymatic_coverage()
screen_vs_assay()
chemical_diversity()
exp7spentmedia.Erectale_growth()
#
# Export to Metabolights
#