[R] More than on loop??

[che]

here you are the whole code, and the data is attached:
> x<-read.table("C:/Uni/502/CA2/hiv.dat", header=TRUE)
> num<-nrow(x)
> AA<-c('A','C','D','E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','Y')
> nc<-x$Label[61:308]
> c<-x$Label[nc]
> noncleaved<-function(x)
+ {
+ y<-matrix(0,20,8)
+ colnames(y)<-c("N4","N3","N2","N1","C1","C2","C3","C4")
+ for(i in 1:num){
+ if (x$Label[i] %in% nc)
+ {
+ for(j in 1:8){
+ res<-which(AA==substr(x$Peptide[i],j,j))
+ y[res, j]=y[res, j]+1
+ }
+ }
+ }
+ return (y/274*100)
+ }
> 
> cleaved<-function(x)
+ {
+ y<-matrix(0,20,8)
+ colnames(y)<-c("N4","N3","N2","N1","C1","C2","C3","C4")
+ for(i in 1:num){
+ if (x$Label[i] %in% nc)
+ {
+ for(j in 1:8){
+ res<-which(AA==substr(x$Peptide[i],j,j))
+ y[res, j]=y[res, j]+1
+ }
+ }
+ }
+ return (y/113*100)
+ }
> 
> hi<-function(x)
+ {
+ height<-rep(0,8)
+ for (j in 1:8){
+ height[j]<-sum(round(cleaved(x)[,j]))
+ max.height<-max(height)
+ }
+ plot(c(0,10*8),c(0,max.height+20),col="white")
+ }
> recta<-function(x)
+ {
+ colmap<-c("#FFFFFF", "#FFFFCC", "#FFFF99", "#FFFF66", "#FFFF33",
+ "#FFFF00", "#FFCCFF", "#FFCCCC", "#FFCC99", "#FFCC66", "#FFCC33",
+ "#FFCC00", "#FF99FF", "#FF99CC", "#FF9999", "#FF9966", "#FF9933",
+ "#FF9900", "#FF33FF", "#FF33CC")
+ for (j in 1:8){
+     xx<-j*10
+ for(k in 1:20){
+         yy<-round(cleaved(x)[k,j])
+         rect(xx,yy,xx+10,yy+round(cleaved(x)[k,j]),col=colmap[k])
+  }
+  }
+  }
-- 
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