object of class LDmat, i.e the output of function pairwiseLD using argument type="matrix".
gpData
object of class gpData with object map or a data.frame with columns 'chr' (specifying the chromosome of the marker) and 'pos' (position of the marker within chromosome measured with genetic or physical distances)
dense
logical. Should density visualization for high-density genetic maps be used?
nMarker
logical. Print number of markers for each chromosome?
centr
numeric vector. Positions for the centromeres in the same order as chromosomes in map. If "maize", centromere positions of maize in Mbp are used.
file
Optionally a path to a file where the plot is saved to
fileFormat
character. At the moment two file formats are supported: pdf and png. Default is "pdf".
…
further graphical arguments for function plot
Value
Plot of neighbour LD along each chromosome. One chromosome is displayed from the first to the last marker.
Details
The plot is similar to plotGenMap with the option dense=TRUE, but here the LD between adjacent markers is plotted along the chromosomes.