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library(circlize)

load(paste0(system.file(package = "circlize"), "/extdata/tp_family.RData"))
df = data.frame(gene = names(tp_family),
                start = sapply(tp_family, function(x) min(unlist(x))),
                end = sapply(tp_family, function(x) max(unlist(x))))

circos.genomicInitialize(df)
circos.genomicTrackPlotRegion(ylim = c(0, 1), 
    bg.col = c("#FF000040", "#00FF0040", "#0000FF40"), 
    bg.border = NA, track.height = 0.05)
    
n = max(sapply(tp_family, length))
circos.genomicTrackPlotRegion(ylim = c(0.5, n + 0.5), 
    panel.fun = function(region, value, ...) {
        gn = get.cell.meta.data("sector.index")
        tr = tp_family[[gn]]  # all transcripts for this gene
        for(i in seq_along(tr)) {
            # for each transcript
            current_tr_start = min(tr[[i]]$start)
            current_tr_end = max(tr[[i]]$end)
            circos.lines(c(current_tr_start, current_tr_end), 
                c(n - i, n - i), col = "#CCCCCC")
            circos.genomicRect(tr[[i]], ytop = n - i + 0.4, 
                ybottom = n - i - 0.4, col = "orange", border = NA)
        }
}, bg.border = NA, track.height = 0.3)
circos.clear()