R/save_roi_testing.R

In danielcanueto/rDolphin: Reliable automatic profiling of 1D 1H NMR Spectra, with additional tools for analysis

#' Saving of results in interface in individual quantification
#'
#' @param provisional_data List with elements to save.
#' @param final_output List with quantifications and indicators of quality of quantification.
#' @param reproducibility_data List with necessary information to load quantifications on the Shiny GUI.
#' @param imported_data List with typical elements necessary to perform quantification of ROIs.
#'
#' @return List with updated final_output and reproducibility_data variables.
#' @export save_roi_testing

save_roi_testing=function(provisional_data,imported_data,final_output,reproducibility_data) {


if (provisional_data$fitting_type == "Clean Sum" ||
    provisional_data$fitting_type == "Baseline Sum") {

  provisional_data$reproducibility_data[[provisional_data$spectrum_index]][[provisional_data$signals_codes]]$ROI_profile=ROI_profile
  provisional_data$reproducibility_data[[provisional_data$spectrum_index]][[provisional_data$signals_codes]]$plot_data=dummy$plot_data
  provisional_data$reproducibility_data[[provisional_data$spectrum_index]][[provisional_data$signals_codes]]$Xdata=Xdata
  provisional_data$reproducibility_data[[provisional_data$spectrum_index]][[provisional_data$signals_codes]]$Ydata=Ydata
  provisional_data$reproducibility_data[[provisional_data$spectrum_index]][[provisional_data$signals_codes]]$results_to_save=results_to_save
  provisional_data$reproducibility_data[[provisional_data$spectrum_index]][[provisional_data$signals_codes]]$error1=results_to_save$fitting_error



} else if (provisional_data$fitting_type == "Clean Fitting" || provisional_data$fitting_type ==
    "Baseline Fitting") {




  for (i in seq_along(provisional_data$signals_codes)) {
    reproducibility_data[[provisional_data$spectrum_index]][[provisional_data$signals_codes[i]]]$ROI_profile=provisional_data$ROI_profile
    reproducibility_data[[provisional_data$spectrum_index]][[provisional_data$signals_codes[i]]]$program_parameters=provisional_data$program_parameters
    reproducibility_data[[provisional_data$spectrum_index]][[provisional_data$signals_codes[i]]]$plot_data=provisional_data$plot_data
    reproducibility_data[[provisional_data$spectrum_index]][[provisional_data$signals_codes[i]]]$Xdata=provisional_data$Xdata
    reproducibility_data[[provisional_data$spectrum_index]][[provisional_data$signals_codes[i]]]$Ydata=provisional_data$Ydata
    reproducibility_data[[provisional_data$spectrum_index]][[provisional_data$signals_codes[i]]]$results_to_save=provisional_data$results_to_save
    reproducibility_data[[provisional_data$spectrum_index]][[provisional_data$signals_codes[i]]]$signals_parameters=provisional_data$signals_parameters
    reproducibility_data[[provisional_data$spectrum_index]][[provisional_data$signals_codes[i]]]$FeaturesMatrix=provisional_data$FeaturesMatrix
    reproducibility_data[[provisional_data$spectrum_index]][[provisional_data$signals_codes[i]]]$error1=provisional_data$error1


  }
  final_output = save_output(
    provisional_data$spectrum_index,
    provisional_data$signals_codes,
    provisional_data$results_to_save,
    imported_data$buck_step,
    final_output)

}



  # tryCatch({write_info(imported_data$export_path, final_output)}, error = function(err) {
  #   print('Not possible to overwrite a csv file open with Microsoft Excel')
  # })

    dummy=list(final_output=final_output,reproducibility_data=reproducibility_data)
    return(dummy)

  }