Nothing
FreqPlotfocal<-function(calls, header="FrequencyPlot focal aberrations"){
Chromo<-chromosomes(calls)
focal.call<-assayDataElement(calls, 'focal')
## Add check for 'focal' within calls
n_sam<-ncol(focal.call)
n<-dim(focal.call)
cat("n", "\t")
Gains<-matrix(data=0, ncol=ncol(calls), nrow=nrow(calls))
Losses<-matrix(data=0, ncol=ncol(calls), nrow=nrow(calls))
Gains[which(focal.call>0)]<- 1
Losses[which(focal.call<0)]<- 1
Gain_sum<-rowSums(Gains)
Loss_sum<-rowSums(Losses)
### Color focals and CNVs
color.gain<-rep("grey", nrow(Gains))
color.gain[which(fData(calls)$CNV==0 & Gain_sum!=0)]<-"red"
color.loss<-rep("grey", nrow(Gains))
color.loss[which(fData(calls)$CNV==0 & Loss_sum!=0)]<-"blue"
#### Plotting
plot((Gain_sum/n_sam)*100, ylim=c(-100,100), type="h", col=color.gain, xlab="Chromosome", ylab="Frequency (Percentage)", main=paste(header),xaxt="n")
points((-Loss_sum/n_sam)*100, type="h", col=color.loss)
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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