Usage
# S3 method for LDmat
plot(x, gpData, plotType = "map", dense = FALSE,
nMarker = TRUE, centr = NULL, chr = NULL,
file = NULL, fileFormat = "pdf", onefile = TRUE, ...)
Arguments
x
Object of class LDmat
, i.e the output of function pairwiseLD
with argument type="matrix"
.
gpData
Object of class gpData
with object map
plotType
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"
).
dense
For plotType="neighbour"
, logical
. Should density visualization for high-density genetic maps be used?
nMarker
For plotType="neighbour"
, logical
. Print number of markers for each chromosome?
centr
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.
chr
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!
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"
.
onefile
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