R/createQCreport.R

In computational-metabolomics/qcrms: Creates quality control output from XCMS output

#' @importFrom rmarkdown render
#' @import captioner
#' @import pmp
#' @import gridExtra
#'
NULL

#' Create a pdf output from data slots on QCreportObject
#'
#' @param QCreportObject Qcreport object
#' @param outputfile Name of the output pdf file
#' @export

createQCreport <- function(QCreportObject, outputfile=NULL) {
  if (is.null(outputfile)) {
    outputfile <- paste(QCreportObject$projectInfo$assay, "pdf", sep=".")
  }

  source(file.path(system.file(package="qcrms"), "captions", "Captions.R"))
  QCrmd <- file.path(system.file(package="qcrms"), "rmd", "QC_report.Rmd")

  rmarkdown::render(QCrmd, output_format="pdf_document",
    output_file=outputfile, output_dir=QCreportObject$projectdir,
    knit_root_dir=QCreportObject$projectdir,
    intermediates_dir=QCreportObject$projectdir, clean=TRUE)

  unlink(file.path(QCreportObject$projectdir, "functions"), recursive=TRUE,
    force=TRUE)
  unlink(file.path(QCreportObject$projectdir, "Processing_steps"),
    recursive=TRUE, force=TRUE)
}