R/calc_norm_OD.R

In padpadpadpad/MicrobioUoE: R package for making our life easier

#' calc_norm_OD
#'
#' Calculates the volumes needed for a set of OD readings to normalise OD across samples
#'
#' @param file_in the filename of the file containing the initial OD readings
#' @param file_out the filename of the file you want to write to. This defaults to appending '_inocs' onto the `file_in` name
#' @param new_sol_conc the desired final concentration of the solution. Defaults to 0.1.
#' @param new_sol_vol the volume of the final solution. Defaults to 1000.
#' @param control the value of the control on the OD reader. Defaults to 0
#' @author Daniel Padfield
#' @details Relies on having a column called OD which contains the initial OD values
#' @return Saves a file with the reuqired inoculum values to normalise OD at a given final volume.
#' @examples
#' \dontrun{calc_norm_OD(file_in = 'OD_start.csv',
#' file_out = 'OD_inocs.csv',
#' new_sol_conc = 0.1,
#' new_sol_vol = 1000,
#' control = 0.035)}
#' @importFrom magrittr '%>%'
#' @name calc_norm_OD
#' @export calc_norm_OD

# quiets concerns of R CMD check re: the .'s that appear in pipelines
if(getRversion() >= "2.15.1")  utils::globalVariables(c(".", 'OD', 'cont', 'OD_cor', 'inoc_samp'))

calc_norm_OD <- function(file_in, file_out, new_sol_conc, new_sol_vol, control){

  # set up defaults
  if(missing(file_out)){file_out <- paste0(tools::file_path_sans_ext(file_in), '_inocs.', tools::file_ext(file_in), sep = '')}
  if(missing(new_sol_conc)){new_sol_conc <-  0.1}
  if(missing(new_sol_vol)){new_sol_vol <- 1000}
  if(missing(control)){control <- 0}

  # load in data ####
  d <- utils::read.csv(file_in, stringsAsFactors = FALSE) %>%
    dplyr::mutate(., cont = (!! control),
           OD_cor = OD - cont)

  # calculate concentrations ####w
  d <- dplyr::mutate(d, dil_fac = OD_cor / (!! new_sol_conc),
              inoc_samp = round(MicrobioUoE::stock_sol_vol(OD_cor, (!! new_sol_conc), (!! new_sol_vol)), 0),
              inoc_diluent = (!! new_sol_vol) - inoc_samp)

  # write csv out
  utils::write.csv(dplyr::select(d, -cont), file_out, row.names = FALSE)

}