R/micropredict.R

In Cascade: Selection, Reverse-Engineering and Prediction in Cascade Networks

#' @rdname plot-methods
setMethod("plot"
          ,c("micropredict")
          ,function(x
                    ,time=NULL
                    ,label_v=NULL
                    ,frame.color="white"
                    ,ini=NULL
                    ,label.hub=FALSE
                    ,edge.arrow.size=0.7
                    ,edge.thickness=1){
	net<-x@network
	micro<-x@microarray_changed
	nv<-x@nv
	micro_pred<-x@microarray_predict
	targets<-x@targets
	O<-net@network
  	Omega<-net@network
    O[abs(O)<nv]<-0
    O[abs(O)>=nv]<-1
    if(is.null(label_v)){label_v<-1:dim(O)[1]}
	
	G<-graph.adjacency(O,weighted=TRUE)
	
	couleur1<-colorRamp(c(grey(0.95),"blue"))
	couleur2<-colorRamp(c(grey(0.95),"red"))
	color<-rep(grey(0.0999),length(V(G)))
	
	if(is.null(ini)){
	P<-position(net,nv)
	}else{
		P<-ini
		}
		
	if(is.null(time)){
		K<-2:(length(micro@time))
		} 		else{K<-time}
		for(time in K){
		if(length(K)>1){
	dev.new()}
		if(time==length(micro@time)){time<-0}
		sup_pred<-1:dim(micro@microarray)[2]
	sup_pred<-sup_pred[sup_pred%%length(micro@time)==time]
	M<-apply(micro@microarray[,sup_pred]-micro_pred@microarray[,sup_pred],1,mean)
	  
	maxi<-round(max(abs(M[-targets])),2)
	if(max(abs(M))!=0){M<-M/max(abs(M[-targets]))}
	long<-1:length(M)
	long<-long[-targets]
	for(j in long){
		
		if(M[j]>0){
			color[j]<-rgb(couleur2(max(M[j],0.2)),alpha=255,maxColorValue=255)
					}
					else{
						color[j]<-rgb(couleur1(max(-M[j],0.2)),alpha=255,maxColorValue=255)

					}
					if(M[j]==0){
            color[j]<- rgb(couleur2(0),alpha=255,maxColorValue=255)
					}
		
	}
	if(!is.null(targets)){color[targets]<-"green"}
	plot(net,nv=nv,color.vertex=color,ini=P,label_v=label_v,frame.color=frame.color,label.hub=label.hub,
	edge.arrow.size=edge.arrow.size,edge.thickness=edge.thickness)
couleur3<-colorRamp(c("blue","grey","red"))
nb.col<-300
coll<-rgb(couleur3(1:nb.col/nb.col),maxColorValue=255)

rect(seq(-1,-0.5,length.out=nb.col)[1:(nb.col-1)],-1,seq(-1,-0.5,length.out=nb.col)[2:nb.col],-0.95,border="transparent",col=coll)
text(-1,-1.05,-maxi)
text(-0.51,-1.05,maxi)
text(-0.751,-1.05,"0")	
if(time==0){time<-length(micro@time)}
 text(-0.8,1.1,paste("Time point prediction =",time, sep=" "))
		}
		
}
)