Plot CNV graphs over an Ideogram

[andrisvAria]

Hello,

I need to create reports that contain two CNV graphs and an Ideogram, for 30 samples.
I have the following code which produces the CNV graph:

one=read.table("$sampleid.chr$chr.$start.signal",sep="\\t")
bmp(filename="$sampleid.chr$chr.$start.$end.CN$cn.bmp",width = 720, height = 720, res=300, pointsize=6)
par(mfrow=c(3,1),las=1,mar=c(4,4.2,1.5,1.3))

a=rep("blue",length(one\$V1))
for(i in 1:length(one\$V1)){
	if(one\$V1[i]>=$start1 & one\$V1[i]<=$end1){
		a[i]="red"
	}
}
plot(one\$V1,one\$V2,pch=20,cex=$cex,ylim=c($lrr_bound,1),ylab="Log R Ratio",xlab="Chr$chr Position ($megabp)",col=a)
title(paste("$sampleid.chr$chr.$start-$end","(CN=$cn)"))
abline(v=c($start1,$end1),col="grey",lty=1,lwd=0.3)
abline(h=0,col="grey",lty=2,lwd=0.3)
plot(one\$V1,one\$V3,pch=20,cex=$cex,ylim=c(0,1),ylab="B Allele Freq",xlab="Chr$chr Position ($megabp)",col=a)
abline(v=c($start1,$end1),col="grey",lty=1,lwd=0.3)

I would like to add the Ideogram of the respective chromosome below these two plots. I set the command par(mfrow=c(3,1),las=1,mar=c(4,4.2,1.5,1.3)) for three rows, so that in the last I get the ideogram.

I visualise the ideogram with this print(plotIdeogram(genome = "hg19"))

but no matter what I have tried, the ideogram refuses to go under the existing plots, instead it overwrites them. Is it possible to manipulate the Ideogram object to make it follow my layout?

[lawremi]

ggbio produces graphics using the grid package, which is different from base graphics. The gridBase package might help you combine them; but I have no experience with it.

[andrisvAria]

Thank you @lawremi , this worked great!