I am looking for some software/R-package that can plot both genetic and physical distances. One way I could think of is having two vertical chromosomes structure side by side - one with horizontal markers according to genetic distances while the other with physical distances. The name of those SNPs can be in the middle serve as a connector. By physical distance of an SNP marker, I mean either just the start position of sequence (or an average of start and end positions of sequence).
The other way I can think of - If there is one single vertical chromosome structure and horizontal markers plotted within this structure that denotes physical positions while on the right side, for each marker pair, the genetic length is shown somehow. i.e, the region with high crossover will have an inflated cM length.
I hope I am not too vague in describing my question. But please do suggest other ideas that integrate both genetic lengths and physical lengths pictorially.
cM, or centiMorgans are a not a real physical distance, rather reflect the recombination frequency between two loci. No one uses cM anymore since we have the whole genome and the data on recombination frequencies are likely not very complete since few labs do these types of mapping experiments anymore.
Gregory Dressler Thanks for your answer. I am working on estimating recombination frequencies between markers and noticed that male and female has quite different frequencies. I was thinking of a way to illustrate the results better by plotting both genetic distances and physical distances and hence was looking for some suggestions. I am hopeful that some of my results will be interesting in terms of sex differences of meiotic recombination within the same species.
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