plotNeighbourLD: Plot neighbour linkage disequilibrium
In synbreed: Framework for the Analysis of Genomic Prediction Data using R

Description Usage Arguments Details Value Author(s) See Also Examples

A function to visualize Linkage Disequilibrium estimates between adjacent markers.

plotNeighbourLD(
  LD,
  gpData,
  dense = FALSE,
  nMarker = TRUE,
  centr = NULL,
  file = NULL,
  fileFormat = "pdf",
  ...
)

`LD`	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`

The plot is similar to plotGenMap with the option dense=TRUE, but here the LD between adjacent markers is plotted along the chromosomes.

Plot of neighbour LD along each chromosome. One chromosome is displayed from the first to the last marker.

Theresa Albrecht and Hans-Juergen Auinger

plotGenMap, pairwiseLD

## Not run: 
library(synbreedData)
data(maize)
maize2 <- codeGeno(maize)
LD <- pairwiseLD(maize2, chr = 1:10, type = "matrix")
plotNeighbourLD(LD, maize2, nMarker = FALSE)

## End(Not run)