R/readjustWindow.R

In protViz/cdsw: Computing Dynamic SWATH Windows

# moves the windows start and end to regions where no peaks are observed
.makenewfromto <- function( windfrom, empty , isfrom=TRUE){
  newfrom <- NULL
  for(from in windfrom){
    idx <- which.min(abs(from - empty))
    startmass <- 0
    if(isfrom){
      if(idx > 1){
        if(empty[idx] < from) {
          startmass <- empty[idx]
        } else {
          startmass <- empty[idx-1]
        }
      }else{
        startmass <- from
      }
    }else{
      if(idx < length(empty)){
        if(empty[idx] > from) {
          startmass <- empty[idx]
        } else {
          startmass <- empty[idx+1]
        }
      }else{
        startmass <- from
      }
    }
    newfrom <- c(newfrom, startmass)
  }
  return(newfrom)
}

#' Readjust windows so that boundaries in regions of few peaks.
#'
#' @param wind a data frame with columns from and to
#' @param ms1data masses
#' @param digits mass accuracy
#' @param maxbin maximum number of bins
#' @param plot diagnostic plots (default FALSE)
#' @export
#' @examples
#'
#' library(cdsw)
#' cdsw <- Cdsw(masses)
#' breaks <- cdsw$sampling_breaks(maxwindow=100,plot=TRUE)
#' table <- cdsw$asTable()
#' dim(table)
#' head(table)
#'
#' tmp <- readjustWindows(table, masses,maxbin=10)
#' data.frame(tmp)
#'
readjustWindows <- function(wind ,ms1data, digits=1, maxbin = 15, plot=FALSE){
  breaks <- seq(round(min(ms1data)-1/10^digits,digits=1),round(max(ms1data)+1/10^digits,digits=1),by=1/10^digits)

  reshist <- graphics::hist(ms1data, breaks=breaks, plot=plot)
  if(plot){
    graphics::abline(v=wind$from,col=2,lty=2)
    graphics::abline(v=wind$to,col=3,lty=2)
  }
  empty <- reshist$mids[which(reshist$counts < maxbin )]
  newfrom <- .makenewfromto(wind$from , empty)
  newto <- .makenewfromto(wind$to , empty , isfrom=FALSE )
  if(plot){
    graphics::plot(reshist,xlim=c(newfrom[round(length(newfrom)/2)]-3,newfrom[round(length(newfrom)/2)]+3))
    graphics::abline(v=empty,col="gray")

    graphics::abline(v = newfrom,lwd=0.5,col="red")
    graphics::abline(v = newto , lwd=0.5,col="green")
    graphics::plot(reshist,xlim=c(newfrom[round(length(newfrom)/4)]-3,newfrom[round(length(newfrom)/4)]+3))
    graphics::abline(v = newfrom,lwd=0.5,col="red")
    graphics::abline(v = newto , lwd=0.5,col="green")
  }
  width <- (newto - newfrom)
  mid <- (newfrom + newto)*0.5
  newCounts <- NULL

  for(i in 1:length(newfrom))
  {
    newCounts <- c(newCounts,sum(ms1data >= newfrom[i] & ms1data <= newto[i]))
  }
  list( from= newfrom,to= newto,mid= mid, width = width, counts = newCounts )
}