modification nom de fonction mcq.plot.area.triplex.effect vers mcq.plot.area.multiplex.effect

MCQR/NAMESPACE

@@ -70,7 +70,7 @@
 	export("mcq.get.protlist")
 
 # Functions mcq.plot
-	export("mcq.plot.aera.triplex.effect")
+	export("mcq.plot.aera.multiplex.effect")
 	export("mcq.plot.cluster")
 	export("mcq.plot.counts.per.injection")
 	export("mcq.plot.global.intensity")

MCQR/R/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)
+}
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