How to superimpose barplots in karyotype graphic using the chromPlot Bioconductor package?
chromPlot(gaps = cel_gap, figCols = 2, annot1 = annot1, annot2 = annot3, annot3 = annot2,
          chrSide=c(1, 1, -1, 1, -1, 1, -1, 1))


The chrSide argument decides on which side the histogram goes, so it can be used to solve my problem. The bars are not stacked but the result is the same: more accurate visualisation. 

Thanks to Llopis for the guidance.