I am using [snp.plotter][1] to illustrate LD heatmaps along side a zoom plot. [Here][2] is an example of what I mean.

However, in [this manuscript][3], they have images that look to be made by snp.plotter, but have gene diagrams overlaid, like can be done in LocusZoom. In [the documentation for snp.plotter][4], however, I cannot find any option to add such a diagram.

Does anyone know how this is being accomplished? I know how to use Image Magick if an ad hoc addition is required, but at present I am not sure if the diagram is being added through the program or by another means... 

  [1]: https://github.com/cannin/snp_plotter
  [2]: https://camo.githubusercontent.com/6c7d77ead2dbe3a360124ac52ff12422c1156b3e/68747470733a2f2f7261772e6769746875622e636f6d2f63616e6e696e2f736e705f706c6f747465722f6d61737465722f646f63732f6e756c6c5f7273715f706879735f636f6c6f722e706e67
  [3]: http://www.nature.com/ng/journal/v46/n9/fig_tab/ng.3052_F1.html
  [4]: https://cran.r-project.org/web/packages/snp.plotter/snp.plotter.pdf
You're correct. snp.plotter does not include a feature to incorporate the LocusZoom plots. Likely, the authors of the article created the two plots and then combined them in Illustrator or Inkscape. snp.plotter can produce PDFs so you would not lose quality by combining the images. 
