I am not sure there is a software that would allow you to generate the entire panel A, but the upper part of panel A can be made from scratch. We would use Canvas after importing the three TIFF images of the primary graphs. 

There are some add-ins on Geneious that may do something similar for you.

Hi John, I actually use Geneious, so can you be more specific on the plug-in that you're referring.

Thanks

I would use R for the three plots and Adobe Illustrator for the upper cartoon and for assembling the figure.

The subgraphs definitely look like R to me. The top bit of A is probably done in Illustrator. It takes a while to put in the lines but I can't think of any software that can do a plot like this without having to use Illustrator at some point.

i agreed with Xavier Sole adobe Illustrator is fit option

I agree with the above - the lower part can be assembled as a heatmap in ggplot2. The genome context plot could probably be partially assembled using ggplot or something similar but it probably isn't worth the time. It might be possible to make the Gviz package in Bioconductor do something like it.

http://www.bioconductor.org/packages/release/bioc/html/Gviz.html