plot.LDmat: Plot function for class 'LDmat'

Description Usage Arguments Details Author(s) See Also

View source: R/plot.LDdf.LDmat.r

Description

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) .

Usage

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## S3 method for class '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

Details

For more details see at plotNeighbourLD or LDMap

Author(s)

Hans-Juergen Auinger

See Also

plotNeighbourLD, LDDist, plotGenMap, pairwiseLD


synbreed documentation built on March 19, 2018, 3 p.m.