Hi, I want to generate a LD plot that looks like the triangle in the lower part of the output of snp.plotter() As I would not use the values of the original LD measure (instead I use a more general measure) I have calulated pairwise "correlation" on my own. I could arrange the results in a data frame like chr1 pos1 snp1 chr2 pos2 snp2 ld Is there a way/ function to generate a LD plot without prior calculation of LD done by R? Which function can I use based on my own calculations? Thanks!