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README.md
calculations.R
gen_times.R
iso_labels.R
plots.R
server.R
table.R
ui.R
widgets.R

README.md

isolabel

A shiny app for estimating expected enrichments from stable isotope labeling in microbial populations. Based on the isotopic enrichment resulting from unbiased clonal growth in the presence of an isotopic label:

equation

with equation the isotopic composition of new biomass generated in the presence of the isotope label (using fractional abundances F is important for correct mass balance!). Substituting the growth rate for the generation time T (µ = ln(2) / T), one can readily calculate the required labeling time to reach a target isotopic composition equation:

equation

This app is intended to make it easy to explore this space for different isotope systems and takes care of all the isotope conversions. There are several ways you can run this app.

Run online

An online version is available here and should run from any javascript enabled browser without installing anything extra (but is not necessarily always the most up to date version although I will try to keep it current).

Run locally

To run the shiny app locally you need to install the following packages:

packages <- c(
  "shiny", "shinydashboard", "shinyBS", "shinyjs", "DT",
  "lubridate", "stringr", "devtools", 
  "reshape2", "plyr", "magrittr", "dplyr",
  "ggplot2", "RColorBrewer")
install.packages(packages, depen=T)
devtools::install_github("isotopia", "sebkopf", "v0.4.1")

Run locally from GitHub

Now you can just run the app either directly from GitHub (most convenient and always up to date):

library(shiny)
runGitHub("sebkopf/shinyApps", subdir = "isolabel")

Run local copy

Or you can copy the server.R and ui.R source files from the isolabel folder to your local workspace directory (e.g. into a folder named isolabel) - or simply fork the entire repository and clone it to your computer - and then run it from this folder (adjust relative path from your working directory):

library(shiny)
path <- "isolabel"
runApp(path)