R/generate_report.R

In MRCIEU/metaboprep: Metabolomics data preparation and processing pipeline

#' generate metaboprep summary html report
#'
#' This function generates the html report.
#'
#' @param full_path_2_Rdatafile full path to the Rdatafile 
#' @param dir_4_report directory to place the report
#' @param path_2_Rmd_template full path to the html report template
#'
#' @keywords knit html report
#'
#' @return Writes a html report to file
#'
#' @importFrom knitr knit2html
#' 
#' @return an html file written to file
#'
#' @export
#'
#' @examples
#' 
#'
generate_report = function(full_path_2_Rdatafile = "ReportData.Rdata", dir_4_report = "./", path_2_Rmd_template = file.path( system.file("rmarkdown", package="metaboprep"), "metaboprep_Report_v0.Rmd" ) ){
   ## package check
   pkgs = c("knitr")
   for(pkg in pkgs){
    if (!requireNamespace( pkg, quietly = TRUE)) {
        stop(paste0("Package \"", pkg,"\" needed for generate_report() function to work. Please install it."),call. = FALSE)
      }
   }

   ## load R data file to environment
   message("Loading the R data file")
   load(full_path_2_Rdatafile)

   ## knit report
   message("knit the report to html")
   knitr::knit2html( 
      input = path_2_Rmd_template,
      output = paste0(dir_4_report, "metaboprep_summary_report.html") 
      )
}