The quantsmooth Bioconductor package also has chromosome plotting functionality in the prepareGenomeplot(), paintCytobands() functions


GenomeGraphs package in Bioconductor allows to draw (human) chromosome ideograms with R



One more for people comfortable with R/BioC and looking for ways to plot various kinds of genomic data is ggbio.

Resource
http://www.biostars.org/p/378/

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