R/IsoPlot.R

In maSigPro: Significant Gene Expression Profile Differences in Time Course Gene Expression Data

IsoPlot <- function(get, name, only.sig.iso=FALSE, ylim=NULL, xlab = "Time",  ylab = "Expression value", points=TRUE, cex.main=3,cex.legend=1.5)
{

 edesign = get$Model$design$edesign
 data <- get$Model$data
 gen <- get$Model$gen

 if(only.sig.iso){
  sig.iso2 <- get$get2$summary
  gen <- as.character(gen[rownames(data)%in%sig.iso2])
  data <- get$get2$sig.genes$sig.profiles
  }

 data = data[gen==name,] 
 nt=nrow(data)
 time = edesign[, 1]
 groups = edesign[, c(3:ncol(edesign))]
 repvect = edesign[, 2]
 n.groups<-ncol(edesign)-2

if(n.groups==1){group=factor(groups, labels=colnames(edesign)[3])}
else group <- factor( as.matrix(edesign[,3:ncol(edesign)])%*%c(1:n.groups), labels=colnames(edesign)[3:ncol(edesign)])

 yy<-as.numeric(data[1,])

    if (n.groups==1) {
        ncol = 1
        codeg =colnames(edesign)[3]
    }
    else {
        ncol = ncol(groups)
        codeg <- as.character(colnames(groups))
    }
if (is.null(ylim)) ylims = c(min(data, na.rm = TRUE), max(data, na.rm = TRUE))

#----------------------------------------------------------------------
# POINTS-PLOT FOR EACH GROUP:
#----------------------------------------------------------------------

 op <- c(5,4,4,0)
 yaxt = NULL
 par(mfrow=c(1,ncol+1))
  
for(i in 1:ncol)
 {
if(ncol==2 && i==2){
 yaxt="n"
 op<-c(5,0,4,4) }

if(ncol>2){
 if(i==ncol){ 
 yaxt="n"
 op<-c(5,0,4,4)
 }
 if(i>1 && i<ncol){ 
 yaxt="n"
 op <- c(5, 2, 4, 2)
 } }
ploti(dati=data[,group==codeg[i]], ti=time[group==codeg[i]], op=op,  ylim=ylims, ylab=ylab, xlab=xlab ,yaxt=yaxt, main=codeg[i], points, cex.main)
}
plot.new()
legend("left",legend=rownames(data),title=" ", cex=cex.legend,,lty=1,col=c(2:(nt+1)),bty="n", lwd=2 )
legend("left",legend=rep(" ",nt),title=name, cex=cex.main, bty="n", title.adj=1)
}


#-------------------------------------------------------------------------------------
# AUXILIAR FUNCTION AUXILIAR ploti()
#-------------------------------------------------------------------------------------
ploti<-function(dati, ti, op, ylim=ylim, ylab=ylab, xlab=xlab ,yaxt=yaxt, main=main, points, cex.main)
{
nt <- nrow(dati)
 y1 <- as.numeric(dati[1,])
 par(mar=op)
 
 tii <- tapply(ti,ti,mean)
 plot(tii,tapply(y1,ti,mean), type="l", ylim=ylim, col=2, xaxt = "n", ylab=ylab, xlab=xlab ,yaxt=yaxt, main=main, cex.main=cex.main)
 axis(1, at = unique(ti), labels = unique(ti))

if(points){
 points(ti, y1, col=2) }

for(j in 2:nt){

 yj <- as.numeric(dati[j,])
 lines(tii,tapply(yj,ti,mean), col=(j+1))
 if(points){
 points(ti, yj, ylim=ylim, col=(j+1)) }
}
}