geneCoverageQC <- function(data.name,sel.gene.name,
legend.layout="topleft",legend.cex=0.5)
# if legend.layout=='none', not plotting legend
{
if(class(data.name)!='PatCNVData')
{
stop('input data.name should be class of "PatCNVData" \n')
}
N_sample <- sampleNum(data.name)
sel.rpkm.mtx <- coverageMatrix(obj=data.name,gene.name=sel.gene.name,
exon.ID.format="gene+pos")
N_sel_exon <- nrow(sel.rpkm.mtx)
samplecolor_vec <- rainbow(N_sample)
comb_exon_names <- rownames(sel.rpkm.mtx)
sample_name_vec <- colnames(sel.rpkm.mtx)
par(oma = c(12, 0, 0, 0))
plot(-1,-1,xlim=c(1,N_sel_exon),ylim=c(0,1.6*max(sel.rpkm.mtx)),
xlab='',ylab='RPKM per exon',xaxt="none")
axis(1, at=seq(1,N_sel_exon),
labels=comb_exon_names, las = 2)
for(j in 1:N_sample)
{
lines(sel.rpkm.mtx[,j],type='b',col=samplecolor_vec[j],pch=j%%26,lwd=1.5,cex=0.8)
}
grid()
if(legend.layout!='none')
{
legend(x=legend.layout,sample_name_vec,
cex=legend.cex,col=samplecolor_vec,pch=seq(1,N_sample)%%26,lty=1,lwd=1)
}
par(oma = c(0, 0, 0, 0)) # restore
} # end of QC function
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.