Genomics. Alignment. Genome. Music. Blast. Bioperl. Python. Cartes. Plot LD in R as in Haploview. If you are particular about an R package, I would like to suggest snp.plotter package.
See snp.plotter reference manual here. Example plot from snp.plotter: Graphviz - Graph Visualization Software. GBrowse. About Generic Genome Browser (GBrowse) GBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on genomes.
Features include: An Easy-On-The-Eye Genome Browser. Cytoscape: Analyzing and Visualizing Network Data. WebLogo - Create Sequence Logos.