Check out this. The first few slides show how to make an ideogram, and they return ggplot2 objects (or that's extractable from a slot of the returned object). Because they return ggplot2 objects, for the relevant chromosome, you can mark the start sites you've got by using a vertical line.
You can use GenomePixelizer to map your genomes to chromosome. Unlike Circos, the tool generate linear chromosome image and the best thing is 'tool generates HTML codes which can be used for making clickable image on embedding some webpages.