R/rawplot.r

In mariev/chromatoplotsgui: Interactive graphics and interface for chromatoplots

#' @export
setGeneric('cgRawPlot', function(object){
  message('No plot method defined!')
  object})


setMethod('cgRawPlot', 'xcmsRaw', function(object){
  print('xcms')
  cgraw <- getcgraw(object)
  qrawplot(cgraw, object@filepath)
  
})

getcgraw <- function(object){
  cgraw <- data.frame(rawMat(object))
  ## add this to match chromatoplots filtering
 # cgraw <- cgraw[cgraw$intensity > quantile(cgraw$intensity, 0.95),]
  ##
  
  col <- log(cgraw[,'intensity'])
  col <- col/max(col)
  cgraw <- qdata(cgraw, size = .1, 
                 color = rgb(1 - col, 1 - col, 0))
  return(cgraw)
}

qrawplot <- function(qd, filepath){
  qscatter( x = time, 
            y = mz, 
            data = qd, 
            main = paste('loadSample: ', filepath),
            xlab="Seconds", 
            ylab="m/z",
            xlim=range(qd$time), 
            ylim=range(qd$mz))
}