I am working with 1001 genomes data for A. thaliana, attempting to look at Linkage Disequilibrium throughout the genome. Using a combination of plink and the LDheatmap package in R, I have successfully generate LD matrices and heatmap figures. Now I would like to overlay gene annotations on the LD heatmap. The LDheatmap package has the ability to load UCSC genomes (or perhaps just the human genome) directly for overlaying annotations, but I do not see how to do this with a custom genome (in this case A. thaliana). I have BED files with all of the annotation information.
I am also open to using another software (other than LDheatmap) that can do this easily. thanks!