karyoploteR

karyoploteR is an R/Bioconductor package to plot genomic data along the genome. It implements a genomic coordinates version of most R graphical primitives facilitating the creation of rich and powerful genome visualizations. Since karyoploteR does not try to "understand" the data it is plotting, it can plot almost anything, any data type,  as long as it is positioned on the genome. In addition, while the package includes data for some of the most used genomes, it can automatically download genome information from external sources and accepts custom genomes directly from the user, thus making it possible to "plot anything on any genome". karyoploteR covers the whole zoom range, going from single base to whole genome changing a single parameter in a function call.  There are additional higher level functions to plot specific types of data, for example one to compute and plot the density of features along the genome, another to plot the coverage level directly from a BAM file or a third one to plot links between genomic regions. 

To know more about the functionality of karyoploteR you can check the package vignette or head to the karyoploteR tutorial page, were you will find a step-by-step tutorial on how to use the package as well as some more involved examples with detailed explanations including how to use karyoploteR to plot different standard data types: RNA-seq differential expression results, SNP-array data, somatic mutation distance using rainfall plots.

Bioconductor landing page: http://bioconductor.org/packages/karyoploteR/

Tuorial and Examples: https://bernatgel.github.io/karyoploter_tutorial/

Source code at github: https://github.com/bernatgel/karyoploteR