R/create_aggregated_uptake_dataset.R

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

#' Calculates the aggregated uptake for peptide pool
#'
#' @param kin_dat single state uptake data, product of e.q.
#' \code{\link{create_uptake_dataset}}
#'
#' @description
#' This is a wrapper function for \code{\link{calculate_aggregated_uptake}},
#' which calculates aggregated uptake for only
#' one time point. This function returns values for all 
#' time points from `kin_dat`.
#' 
#' @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")
#' create_aggregated_uptake_dataset(kin_dat)
#' }
#' 
#' @export

create_aggregated_uptake_dataset <- function(kin_dat){

  kin_dat <- as.data.table(kin_dat)
  times <- unique(kin_dat[["Exposure"]])

  uc_dataset <- lapply(times, function(time){

    uc_t <- calculate_aggregated_uptake(kin_dat,
                                        time_t = time)

  }) %>% bind_rows()

  return(uc_dataset)

}


#' Show aggregated values in friendly form
#' 
#' @param aggregated_dat aggregated uptake data
#' @param differential indicator if the aggregated_dat is 
#' single-state or differential 
#' @param theoretical \code{logical}, determines if values are theoretical
#' @param fractional \code{logical}, determines if values are fractional
#' 
#' @description Function plots the aggregated uptake data
#' with regard to submitted parameters in a friendly form.
#' Designed for GUI.
#' 
#' @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)
#' show_aggregated_uptake_data(aggregated_dat)
#' 
#' diff_uptake_dat <- create_diff_uptake_dataset(alpha_dat)
#' aggregated_diff_dat <- create_aggregated_diff_uptake_dataset(diff_uptake_dat)
#' show_aggregated_uptake_data(aggregated_diff_dat, differential = TRUE)
#' }
#' 
#' @export

show_aggregated_uptake_data <- function(aggregated_dat, 
                                        differential = FALSE,
                                        fractional = TRUE,
                                        theoretical = FALSE){
  
  value <- get_uptake_name(fractional = fractional, 
                           theoretical = theoretical, 
                           differential = differential)
    
  err_value <- get_uptake_error_name(value = value)
    
  value_label <- get_uptake_label(fractional = fractional, 
                                  theoretical = theoretical, 
                                  differential = differential)

  err_value_label <- get_uptake_error_label(value = value_label)

  ##
  
  tmp_dat <- as.data.table(aggregated_dat)
  
  tmp_dat <- tmp_dat[, .(position, aa, Exposure, 
                         val = get(value), err_val = get(err_value))]
  
  tmp_dat[, `:=`(val = round(val, 4),
                 err_val = round(err_val, 4))]
  
  setnames(tmp_dat,
           c("position", "aa", "val", "err_val"),
           c("Position", "Amino", value_label, err_value_label))
  
  tmp_dat <- as.data.frame(tmp_dat)
  
  return(tmp_dat)
  
}