Nothing
FreqPlot<-function(calls, header="FrequencyPlot all aberrations"){
Chromo<-chromosomes(calls)
Calls<-calls(calls)
n_sam<-ncol(Calls)
Gains<-matrix(data=0, ncol=ncol(Calls), nrow=nrow(Calls))
Losses<-matrix(data=0, ncol=ncol(Calls), nrow=nrow(Calls))
Gains[which(Calls>0)]<- 1
Losses[which(Calls<0)]<- 1
Gain_sum<-rowSums(Gains)
Loss_sum<-rowSums(Losses)
#### Plotting
plot((Gain_sum/n_sam)*100, ylim=c(-100,100), type="h", col="red", xlab="Chromosome", ylab="Frequency (Percentage)", main=paste(header),xaxt="n")
points((-Loss_sum/n_sam)*100, type="h", col="blue")
abline(h=0, cex=4)
uni.chr<-unique(Chromo)
temp<-rep(0,length(uni.chr))
for (i in 1:length(uni.chr)){
temp[i]<-max(which(uni.chr[i]==Chromo))}
for (i in 1:length(temp)){
abline(v=temp[i], col="black", lty="dashed")}
# ADD LABELS AND LINES
nChroms<-length(unique(Chromo))
begin<-c()
for (d in 1:nChroms){
chrom <- sum(Chromo == d)
begin <- append(begin,chrom)
}
uni.chr<-unique(Chromo)
temp2<-rep(0,length(uni.chr))
for (i in 1:length(uni.chr)){
if(i==1){
temp2[1] <- (begin[1]*0.5)}
else if(i>1){
temp2[i]<- temp[i-1]+(begin[i]*0.5)}
}
for (i in 1:length(temp)){
axis(1,at=temp2[i],labels=uni.chr[i],cex.axis=1)
}
}
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