LDmat
A function to visualize Linkage Disequilibrium estimates between adjacent markers or isualization of pairwise Linkage Disequilibrium (LD) estimates generated by function pairwiseLD
in a LD heatmap for each chromosome using the LDheatmap
package (Shin et al, 2006) .
# S3 method for LDmat
plot(x, gpData, plotType = "map", dense = FALSE,
nMarker = TRUE, centr = NULL, chr = NULL,
file = NULL, fileFormat = "pdf", onefile = TRUE, ...)
Object of class LDmat
, i.e the output of function pairwiseLD
with argument type="matrix"
.
Object of class gpData
with object map
You can decide, if you like to have a plot with the LD of the neighbouring markers (option "neighbour"
), or you like to have a heatmap of the LD (default option "map"
).
For plotType="neighbour"
, logical
. Should density visualization for high-density genetic maps be used?
For plotType="neighbour"
, logical
. Print number of markers for each chromosome?
For plotType="neighbour"
, numeric
vector. Positions for the centromeres in the same order as chromosomes in map
. If "maize"
, centromere positions of maize in Mbp are used.
For plotType="map"
, numeric
scalar or vector. Return value is a plot for each chromosome in chr
. Note: Remember to add in a batch-script one empty line for each chromosome, if you use more than one chromosome!
Optionally a path to a file where the plot is saved to
character
. At the moment two file formats are supported: pdf and png. Default is "pdf"
.
logical
. If fileFormat = "pdf"
you can decide, if you like to have all graphics in one file or in multiple files.
Further arguments that could be passed to function LDheatmap
For more details see at plotNeighbourLD
or LDMap