mcq_plot_aera_multiplex_effect.R

### method to plot area in log by triplex to show if there is a specifique effect for each triplex


mcq.plot.aera.multiplex.effect <- function(object, file=NULL, binwidth=0.25, type="histogram") {
  
  error_messages <- list()
  j=1
  # if (!is.numeric(class)&!is.null(class)){
  #   error_messages[[j]] <- "class argument must be numeric"
  #   j=j+1
  # }
  if (!is.numeric(binwidth)){
    error_messages[[j]] <- "binwidth argument must be numeric"
    j=j+1
  }
  if(!is.character(file)&!is.null(file)){
    error_messages[[j]] <- "file argument must be characters"
    j=j+1
  }
  if (!(type %in% c("histogram", "density", "experimental"))){
    error_messages[[j]] <- "file argument must be characters"
    j=j+1
  }
  if (length(error_messages) != 0){
    stop(paste("Error on argument format:\n", paste(error_messages, collapse="\n"), sep=""))
  }
  # if(class(object) == "cmcq.pepq.sds"){
  #   if(class(object[[1]]) %in% c("cmcq.pepq.masschroq.labeling","cmcq.pepq.masschroq")){
  #     ## preparing data 
  #     data <- mcq.union.fraction.sds.corrected(object, verbose=FALSE)[[1]]
  #     inj <- data@metadata@injections
  #     meta <- data@metadata@metadata
  #     ### workaround because meta contains fraction column if generated with mcq.union.fraction.sds
  #     if("fraction" %in% colnames(meta)){
  #       meta <- meta[,-which(colnames(meta) %in% "fraction")]
  #     }
  #     inj$msrun_label <- paste(inj$msrun, inj$label, sep="_")
  #     meta <- cbind(inj, meta)
  #     pep <- as.data.table(data@peptides)
  #     meta <- as.data.table(meta)
  #     pep <- merge(pep, meta)
  #   }
  # }else 
  if (class(object) == "cmcq.pepq.masschroq.labeling"){
    inj <- object@metadata@injections
    meta <- object@metadata@metadata
    ### workaround because meta contains fraction column if generated with mcq.union.fraction.sds
    if("fraction" %in% colnames(meta)){
      meta <- meta[,-which(colnames(meta) %in% "fraction")]
    }
    inj$msrun_label <- paste(inj$msrun, inj$label, sep="_")
    meta <- cbind(inj, meta)
    pep <- as.data.table(object@peptides)
    meta <- as.data.table(meta)
    pep <- merge(pep, meta)
  }else{
    stop(paste("the class \"", class(object),"\" is not taken into account by mcq.plot.aera.triplex.effect",sep=""))
  }
  
  p<- list()
  if(type == "histogram"){
    temp <- ggplot(pep, aes(x=logarea, fill=track))+geom_histogram(position= position_dodge2(padding= 0.1), binwidth = binwidth)+xlab("log10(area)")
    temp <- temp + ggtitle("Distribution of log10(area) by triplex")
    p[[1]] <- temp
  }else if(type == "density"){
    temp <- ggplot(pep, aes(x=logarea, fill=track, color=track))+geom_density(alpha=0.1)
    temp <- temp + ggtitle("Distribution of log10(area) by triplex")
    p[[1]] <- temp
  }else if(type == "experimental"){
    toplot <- priv.mcq.compute.hist(as.data.frame(pep), class=20, by="track", value="logarea")
    temp <-ggplot(toplot, aes(x=mids,  y=count, fill=track))+geom_bar(stat="identity", position=position_dodge2(padding=0.2))+ theme(axis.text.x = element_text(angle = 90, hjust = 1))+xlab("log10(area)")+ylab("count")
    temp <- temp + ggtitle("Distribution of log10(area) by triplex")
    p[[1]] <- temp
  }
  
  priv.mcq.visualisation.graph(p, file)
}