Plotting Genomic Overlaps with GRanges

Question

[joe_genome]

I have come up with two approaches using two different findOverlaps methods (Genomic Alignments R package) for which I have opted to use subsetbyOverlaps as this suits my needs better. I'm trying to plot the genomic coordinates that overlap, was trying with the GViz package but not sure if this is suitable.

Wondering what others have done about this?

I have created two separate BAM Files as input which I'ver converted into GRanges objects for further manipulation:

BAM1 <-  readGAlignments(BAM1, use.names=T, param=ScanBamParam(what=c("seq", "mapq", "flag", "isize", "qual")))

BAM2 <-  readGAlignments(BAM1, use.names=T, param=ScanBamParam(what=c("seq", "mapq", "flag", "isize", "qual")))

BAM1_Range  <- as(BAM1, "GRanges")
BAM2_Range  <- as(BAM2, "GRanges")
overlap_regions <- subsetByOverlaps(BAM1_Range, BAM2_Range)

Thanks :)