R/saveSingleFileMultiEIC.R

In peakPantheR: Peak Picking and Annotation of High Resolution Experiments

#' Save to disk a plot of all ROI EIC and detected feature range
#'
#' Plot and save a \code{.png} of all ROI (x is RT, y is intensity), with the matching detected peak rt and peakwidth under it.
#'
#' @param ROIsDataPoint (list) a list of \code{data.frame} of raw data points for each ROI (retention time "rt", mass "mz" and intensity "int" (as column) of each raw data points (as row)).
#' @param curveFit (list) a list of \code{peakPantheR_curveFit} or NA for each ROI
#' @param foundPeakTable (data.frame) \code{data.frame} as generated by \code{\link{findTargetFeatures}}, with features as rows and peak properties as columns. The following columns are mandatory: \code{cpdID}, \code{cpdName}, \code{rt}, \code{rtmin}, \code{rtmax}, \code{mzmin}, \code{mzmax}.
#' @param savePath (str) Full path to save a \emph{.png} of all ROI EICs , expect \code{'filepath/filename.png'}.
#' @param width (float) Width in cm for a single ROI plot (if more than one plot in total, 2 columns will be used). dpi set to a 100.
#' @param height (float) height in a cm for a single ROI plot. dpi set to 100
#' @param verbose (bool) if TRUE message progress
#'
#' @return None
saveSingleFileMultiEIC   <- function(ROIsDataPoint, curveFit, foundPeakTable, savePath, width=15, height=15, verbose=TRUE) {

  ## check input
  nbROI   <- length(ROIsDataPoint)
  if (nbROI != dim(foundPeakTable)[1]) {
    stop('Number of ROI datapoints in "ROIsDataPoint" (', nbROI, ') and features in "foundPeakTable" (', dim(foundPeakTable)[1], ') do not match!')
  }
  if (nbROI != length(curveFit)) {
    stop('Number of ROI datapoints in "ROIsDataPoint" (', nbROI, ') and fitted curves in "curveFit" (', length(curveFit), ') do not match!')
  }

  ## Generate each ROI plot
  p_all         <- vector("list", nbROI)
  for (i in 1:nbROI) {
    p_all[[i]]  <- plotEICDetectedPeakwidth(ROIDataPointSampleList = list(ROIsDataPoint[[i]]),
                                            cpdID = foundPeakTable$cpdID[i],
                                            cpdName = foundPeakTable$cpdName[i],
                                            rt = foundPeakTable$rt[i], 
                                            rtMin = foundPeakTable$rtMin[i],
                                            rtMax = foundPeakTable$rtMax[i],
                                            mzMin = foundPeakTable$mzMin[i], 
                                            mzMax = foundPeakTable$mzMax[i], 
                                            ratio=0.85, 
                                            curveFitSampleList = list(curveFit[[i]]),
                                            sampling=250, sampleColour='black', verbose=verbose)
  }

  ## Set save parameters
  targetFolder  <- dirname(savePath)
  targetFile    <- basename(savePath)
  nSubplot      <- length(p_all)

  if (nSubplot==1) {
    ncol    <- 1
  } else {
    ncol    <- 2
    nrow    <- ceiling(nSubplot/2)
    width   <- width * ncol
    height  <- height * nrow
  }

  ## Save
  ggplot2::ggsave(file=targetFile, plot=gridExtra::arrangeGrob(grobs=p_all, ncol=ncol), device='png', path=targetFolder, dpi=100, width=width, height=height, units='cm', limitsize=FALSE)

  if (verbose) { message('Summary EIC plot saved at: ', savePath)}
}