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 (http://www.atgc.org/GenomePixelizer/GenomePixelizer_Welcome.html) to map your genomes to chromosome. Unlike Circos (http://circos.ca/), 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.