R/chromatoplotsgui.r

In mariev/chromatoplotsgui: Interactive graphics and interface for chromatoplots

#' @title chromatoplotsgui
#' @param dir path to directory where experiment is located
#' @param fly perform data calculations on the fly or instantiate with complete data pipeline?
#' @param guidata output from another instance of cpgui
#' @param ... passed to cgui.meta$new()
#' @return environment containing QWidgets and ChromPlotGUIProperties
#' @export
#' @author Marie Vendettuoli \email{mariecv26@@gmail.com}
chromatoplotsgui <- function(dir = NULL, fly = TRUE, guidata = NULL,...){
  
  .cguienv <- mutalist(w = NULL, cpdata = NULL)
  # if a working dir is not given, open empty dashboard,
  # otherwise use dir contents to start an instance.
  if(is.null(dir)){
    .openemptygui(.cguienv)
    if(!is.null(guidata)){
      .cguienv$cpdata <- guidata
      print(class(.cguienv$cpdata))
      .drawfigs(.cguienv)
      
    }
  }else{
    .checkdirargs(dir)
    .openemptygui(.cguienv)
    .popgui(.cguienv, dir, fly,...)
  }
  
  return( cgui.meta$new(dirloc = NULL, 
                        loadstep = .cguienv$cpdata$loadstep, 
                        loadmethod = .cguienv$cpdata$loadmethod,
                        loadparam = .cguienv$cpdata$loadparam,
                        includeMSn = .cguienv$cpdata$includeMSn, 
                        loaddata = .cguienv$cpdata$loaddata,    
                        loadplot = lapply(1:length(.cguienv$cpdata$loadplot), 
                                          FUN = function(x){return(qdata(strip_mf_df(.cguienv$cpdata$loadplot[[x]]), 
                                                                         size = .5, 
                                                                         color = log(intensity)))}),
                        ## end loadSample params
                        
                        ## params for genProfile
                        step = .cguienv$cpdata$step,       
                        baselevel = .cguienv$cpdata$baselevel,
                        basespace = .cguienv$cpdata$basespace, 
                        integrate = .cguienv$cpdata$integrate,                                                            
                        #                                      profMethod = "character",
                        genprofdata = .cguienv$cpdata$genprofdata,
                        genprofplot = lapply(1:length(.cguienv$cpdata$genprofplot), 
                                             FUN = function(x){return(qdata(strip_mf_df(.cguienv$cpdata$loadplot[[x]]),
                                                                            size = .5, 
                                                                            color = log(intensity)))}),   
                        ## end genProfile
                        
                        ## params for removeBaseline
                        rmbaseMethod = .cguienv$cpdata$rmbaseMethod,   
                        mzrad = .cguienv$cpdata$mzrad, 
                        scanrad = .cguienv$cpdata$scanrad,
                        span = .cguienv$cpdata$span, 
                        runs = .cguienv$cpdata$runs, 
                        b = .cguienv$cpdata$b,
                        rmbasedata = .cguienv$cpdata$rmbasedata,
                        rmbaseplot = lapply(1:length(.cguienv$cpdata$rmbaseplot), 
                                            FUN = function(x){return(qdata(strip_mf_df(.cguienv$cpdata$rmbaseplot[[x]])))})))
}

# check that ...
# 1. dir contains dir (expdesign) or .cdf files (no exp design)
.checkdirargs <- function(dir){
  # save the current working directory location
#   curwd <- getwd()
#   
#   setwd(dir)
#   fileinfos <- file.info(dir)$isdir
#   if(!length(fileinfos[fileinfos]) %in% c(0, length(dir()))){
#       stop('chromatoplotsgui: dir argument must be exp design or CDF files!!')
#   } else {
#       if(length(fileinfos[fileinfos]) == 0){
#         sapply(dir(), FUN = function(x){.checkCDF})
#       }     
#   }
  # navigate back to current working directory
#   setwd(curwd)  
}
## check that file is of type .CDF
.checkCDF <- function(x){
    if(strsplit(x, "\\.")[[2]] != "CDF"){
        stop('chromatoplotsgui: indiv files must be of type .CDF !!')
    }
}

## populate the gui 
.popgui <- function(.cguienv, dir, fly,...){

  message('instantiating chromatoplotsgui: this may take some time...')

  # instantiate new cgui item
  .cguienv$cpdata <- cgui.meta$new(dirloc = dir,...)  
  
  # calculate the loadSample objects
  .poploadsamples(.cguienv, fly, dir)
  
  # calculate the genProfile objects
  .popgenprofile(.cguienv, fly)
  
  # calculate the removeBaseline objects
  .popremovebase(.cguienv, fly)
  
  # calculate qdata objects
  .calcqdata(.cguienv, fly)
  
  
  # draw the cranvas elements
  print(class(.cguienv$cpdata))
  .drawfigs(.cguienv)
  
  message('chromatoplotsgui ready to use!!')
}