yes, but the outcome graphs are almost the same, that mean it does not
calculated in a cumulative way , if you apply the following code, then run
hi(x), and then recta(x), you will see how the shape are similar to the
frequency of Amino Acid in the matrix. i am looking for a code that can do
this automatically starting from the first column ending with the last
column- data attached. many thanx
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")
}
suma<-function(i,j,A)
{
if( j<= 0)
{
sum<-0
}
else
{
sum<-0
for(k in 1:j)
{
sum<- sum + round(A[k,i])
}
}
return(sum)
}
grafica<- function(A)
{
for(i in 1:8)
{
for(j in 1:20)
{
rect((i-1)*10,suma(i,j-1,A),((i-1)*10)+10,suma(i,j,A), col=colmap[j])
if ( A[j,i] != 0)
{
text( ((i-1)*10)+5, (suma(i,j-1,A) + round(A[j,i])/2), amino.acid[j],
cex=( (2*round(A[j,i])/round(max(A))
)))
}
}
}
}
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")
rect(1*10,20,10+10,20+round(cleaved(x)[1,1]),col=colmap[1])
rect(1*10,40,10+10,40+round(cleaved(x)[2,1]),col=colmap[2])
rect(1*10,53,10+10,53+round(cleaved(x)[3,1]),col=colmap[3])
rect(1*10,63,10+10,63+round(cleaved(x)[4,1]),col=colmap[4])
rect(1*10,69,10+10,69+round(cleaved(x)[5,1]),col=colmap[5])
rect(1*10,73,10+10,73+round(cleaved(x)[6,1]),col=colmap[6])
rect(1*10,85,10+10,85+round(cleaved(x)[7,1]),col=colmap[7])
rect(1*10,89,10+10,89+round(cleaved(x)[8,1]),col=colmap[8])
rect(1*10,96,10+10,96+round(cleaved(x)[9,1]),col=colmap[9])
rect(1*10,110,10+10,110+round(cleaved(x)[10,1]),col=colmap[10])
rect(1*10,118,10+10,118+round(cleaved(x)[11,1]),col=colmap[11])
rect(1*10,123,10+10,123+round(cleaved(x)[12,1]),col=colmap[12])
rect(1*10,144,10+10,144+round(cleaved(x)[13,1]),col=colmap[13])
rect(1*10,149,10+10,149+round(cleaved(x)[14,1]),col=colmap[14])
rect(1*10,158,10+10,158+round(cleaved(x)[15,1]),col=colmap[15])
rect(1*10,170,10+10,170+round(cleaved(x)[16,1]),col=colmap[16])
rect(1*10,198,10+10,198+round(cleaved(x)[17,1]),col=colmap[17])
rect(1*10,213,10+10,213+round(cleaved(x)[18,1]),col=colmap[18])
rect(1*10,225,10+10,225+round(cleaved(x)[19,1]),col=colmap[19])
rect(1*10,229,10+10,225+round(cleaved(x)[20,1]),col=colmap[20])
}
http://n4.nabble.com/file/n1312372/hiv.dat hiv.dat
http://n4.nabble.com/file/n1312372/hiv.txt hiv.txt
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