The Gviz package is great - thank you Florian and Robert :-)

    seqinfo <- GenomeInfoDb::seqinfo(BSgenome.Mmusculus.UCSC.mm10::Mmusculus)
    grA <- GenomicRanges::GRanges(
               'chr1', c('4712628-4712643', '4712428-4712627'), '+', seqinfo = seqinfo)
    grB <- GenomicRanges::GRanges(
               'chr1', c('5250212-5250227', '5250012-5250211'), '-', seqinfo = seqinfo)

    ideogram   <- Gviz::IdeogramTrack(genome = 'mm10', chromosome = 'chr1')
    genomeaxis <- Gviz::GenomeAxisTrack()
    siteA     <- Gviz::AnnotationTrack(grA, name = 'siteA')
    siteB     <- Gviz::AnnotationTrack(grB, name = 'siteB')

    pA <- Gviz::plotTracks(list(ideogram, genomeaxis, siteA))  # Works great
    pB <- Gviz::plotTracks(list(ideogram, genomeaxis, siteB))  # Works great too

But how do I capture the generated plots, so that I can re-arrange them together into a multipanelfigure?

    gridExtra::grid.arrange(pA, pB)
    Error in gList(list(chr1 = new("IdeogramTrack", bandTable = list(chrom = c(1L,  : 
    only 'grobs' allowed in "gList"

Thanks. We are happy you like it.

What about this?

grid.newpage()
# 2x2 layout
pushViewport(viewport(layout=grid.layout(2, 2)))
# 1,1 first plot
pushViewport(viewport(layout.pos.col=1,layout.pos.row=1))
Gviz::plotTracks(list(ideogram, genomeaxis, siteA), add=TRUE)
popViewport()
# 2,2 second plot
pushViewport(viewport(layout.pos.col=2,layout.pos.row=2))
Gviz::plotTracks(list(ideogram, genomeaxis, siteB), add=TRUE)
popViewport()
popViewport()