R/prepare_hdxviewer_export.R

In HaDeX2: Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data

#' Prepares data export for HDX-Viewer
#'
#' @param x_dat one state deuterium uptake data or differential uptake data
#' @param differential indicator of x_dat type
#' @param fractional indicator if fractional values are used
#' @param theoretical indicator if theoretical values are used
#' @param download indicator if the result should be downloaded as csv file
#' @param file_path path for saving downloaded file
#' 
#' @importFrom utils write.csv
#' 
#' @description This function produces the data in format suitable for HDX-Viewer.
#' If necessary, this result can be downloaded as the csv file with download indicator 
#' set to true.
#' 
#' @return a \code{\link{data.frame}} object
#'
#' @examples
#' \donttest{
#' # disabled due to long execution time 
#' 
#' kin_dat <- create_uptake_dataset(alpha_dat, states = "Alpha_KSCN" )
#' aggregated_dat <- create_aggregated_uptake_dataset(kin_dat)
#' diff_uptake_dat <- create_diff_uptake_dataset(alpha_dat)
#' diff_aggregated_dat <- create_aggregated_diff_uptake_dataset(diff_uptake_dat)
#' prepare_hdxviewer_export(aggregated_dat, differential = FALSE)
#' # prepare_hdxviewer_export(aggregated_dat, differential = TRUE) # shouldnt work
#' prepare_hdxviewer_export(diff_aggregated_dat, differential = TRUE)
#' # prepare_hdxviewer_export(aggregated_dat, differential = FALSE, download = TRUE) # writes a file
#' 
#' }
#' 
#' @export


prepare_hdxviewer_export <- function(x_dat,
                                     differential = FALSE,
                                     fractional = TRUE,
                                     theoretical = FALSE,
                                     download = FALSE,
                                     file_path = tempdir()){

  x_dat <- as.data.table(x_dat)

  if(differential){

    if(!any(startsWith(names(x_dat), "diff") )){
      stop("Parameters are in conflict with supplied data.")
    }

    if(fractional){

      if(theoretical){

        x_dat <- x_dat[, .(position, diff_theo_frac_deut_uptake, Exposure)]
        x_dat[, diff_theo_frac_deut_uptake:=diff_theo_frac_deut_uptake/100]
        x_dat[, diff_theo_frac_deut_uptake:=round(diff_theo_frac_deut_uptake, 3)]
        value <- "diff_theo_frac_deut_uptake"
      } else {

        x_dat <- x_dat[, .(position, diff_frac_deut_uptake, Exposure)]
        x_dat[, diff_frac_deut_uptake:=diff_frac_deut_uptake/100]
        x_dat[, diff_frac_deut_uptake:=round(diff_frac_deut_uptake, 3)]
        value <- "diff_frac_deut_uptake"
      }
    } else {

      x_dat <- x_dat[, .(position, diff_deut_uptake, Exposure)]
      x_dat[, diff_deut_uptake:=round(diff_deut_uptake, 3)]
      value <- "diff_deut_uptake"

      if(theoretical){

        x_dat <- x_dat[, .(position, diff_theo_deut_uptake, Exposure)]
        x_dat[, diff_theo_deut_uptake:=round(diff_theo_deut_uptake, 3)]
        value <- "diff_theo_deut_uptake"

      }
    }

  } else {

    if(fractional){

      if(theoretical){

        x_dat <- x_dat[, .(position, theo_frac_deut_uptake, Exposure)]
        x_dat[, theo_frac_deut_uptake:=theo_frac_deut_uptake/100]
        x_dat[, theo_frac_deut_uptake:=round(theo_frac_deut_uptake, 3)]
        value <- "theo_frac_deut_uptake"

      } else {

        x_dat <- x_dat[, .(position, frac_deut_uptake, Exposure)]
        x_dat[, frac_deut_uptake:=frac_deut_uptake/100]
        x_dat[, frac_deut_uptake:=round(frac_deut_uptake, 3)]
        value <- "frac_deut_uptake"

      }
    } else {

      x_dat <- x_dat[, .(position, deut_uptake, Exposure)]
      x_dat[, deut_uptake:=round(deut_uptake, 3)]
      value <- "deut_uptake"

      if(theoretical){

        x_dat <- x_dat[, .(position, theo_deut_uptake, Exposure)]
        x_dat[, theo_deut_uptake:=round(theo_deut_uptake, 3)]
        value <- "theo_deut_uptake"

      }

    }

  }

  ## changed to seconds
  x_dat[, Exposure:=Exposure*60]
  x_dat[, Exposure:=paste0(Exposure, "s")]
  x_dat[, .(Residues=position)]
  setnames(x_dat, "position", "Residues")

  res <- dcast(x_dat, Residues ~ Exposure, value.var = value)


  if(download) {
    write.csv(res, paste0(file_path, "\\", value, ".csv"), row.names = FALSE, quote = FALSE)

  }

  return(res)

}