Hello,
I have a plenty of scaffold and contig names which are non-numeric like Scaffold1 (or any other name. That's why I cannot replace them with number since I have names like Fvb1 etc) instead of "1". 

So, can somebody offer a package in R to get Manhattan plots with non-numeric chromosome identifiers? Also, the x axis should be adjustable and not limited to fixed chr number. 

Thanks!
Solved. I used this [GGplot2 Manhattan Plot Function][1]. Thanks to authors!


  [1]: https://github.com/pcgoddard/Burchardlab_Tutorials/wiki/GGplot2-Manhattan-Plot-Function