R/instantiateqdata.r

In mariev/chromatoplotsgui: Interactive graphics and interface for chromatoplots

.calcqdata <- function(.cguienv, fly){
  if(fly){
    .calcqdataLoad(.cguienv, list(.cguienv$cpdata$loaddata[[1]]))
    .calcqdataGen(.cguienv, list(.cguienv$cpdata$genprofdata[[1]]))
    .calcqdataRmBase(.cguienv, list(.cguienv$cpdata$rmbasedata[[1]]), 
                     list(.cguienv$cpdata$genprofdata[[1]]))
    
  } else {
    .calcqdataLoad(.cguienv, .cguienv$cpdata$loaddata)
    .calcqdataGen(.cguienv, .cguienv$cpdata$genprofdata)
    .calcqdataRmBase(.cguienv, .cguienv$cpdata$rmbasedata, .cguienv$cpdata$genprofdata)
  }
}

.calcqdataLoad <- function(.cguienv, x){
  .cguienv$cpdata$loadplot <- lapply(x, FUN = function(y){qdata(rawMat(y), 
                                                size = .5, color = log(intensity))})
}

.calcqdataGen <- function(.cguienv, x){
  .cguienv$cpdata$genprofplot <- lapply(x, FUN = function(y){
    prof <- y@env$profile
    minprof <- ifelse(min(prof)>=0, min(prof),  0)
    temp <- data.frame(time = rep(y@scantime, each = nrow(prof)),
                     mz = rep(profMz(y), ncol(prof)),
                     intensity = as.vector(prof))
    qdata(temp[prof > minprof,], size = .5, color = log(intensity))
  })
}

.calcqdataRmBase <- function(.cguienv, prof, raw){
  if(length(prof) != length(raw)) stop("args must be of same length")
  
  .cguienv$cpdata$rmbaseplot <- lapply(1:length(prof), FUN = function(x){qdata(data.frame(x = 1:10, y = 11:20))
#     time <- raw[[x]]@scantime
#     mzmin <- raw[[x]]@mzrange[1]
#     rawint <- raw[[x]]@env$profile[mz-mzmin+1,]
#     chrom <- data.frame(time = time, intensity = rawint)
#     #p <- qplot(time,rawint,data=chrom,geom="point")
#     #p$title=NULL
#     corint <- object[[x]]@env$profile[mz-mzmin+1,]
#     if (subtract) {
#       res <- corint
#       fit <- rawint - corint
#     } else {
#       res <- rawint - corint
#       fit <- corint
#     }
#     qdata(data.frame( time = rep( raw[[x]]@scantime, 
#                                   each = nrow(raw[[x]]@env$profile)),
#                       mz = rep( seq(from = raw[[x]]@mzrange[1], 
#                                     to = raw[[x]]@mzrange[2]), 
#                                 ncol(raw[[x]]@env$profile)),
#                       prof = as.vector(prof[[x]]@env$profile),
#                       raw = as.vector(raw[[x]]@env$profile)), size = .5)
  })
}