Chromosome or group specific LD heatmaps

If you work on genomics, chances are you have to create an LD heatmap figure sooner or later. I am sure you have used the R package LDheatmap or have thought of using it at some point. The only problem is that despite being a sweet (not necessarily fast) program, it does have its limitations. The biggest one being production of publication-worthy graphics.

To give you an example, look at the following LD heatmap it produced with my mock data. My mock data has 7 chromosomes with 10 markers on each chromosome.

Here is the input data in Excel format.

Continue reading