link.map.cross {wgaim}R Documentation

Plot a genetic linkage map

Description

Neatly plots the genetic linkage map with marker locations and marker names.

Usage

## S3 method for class 'cross':
link.map(object, chr, max.dist, marker.names = TRUE,
tick = FALSE, ...)

Arguments

object object of class "cross"
chr character string naming the subset of chromosomes to plot
max.dist a numerical value in cM determining the distance the genetic map should be subsetted by
marker.names logical value. If TRUE then marker names are plotted alongside each chromosome on the left. Defaults to TRUE
tick logical value. If TRUE then an axis with tick marks are generated for the chromosome names
... arguments passed to "plot" to set up the plot region. Arguments may also be passed to "text" for the manipulation of the marker names

Details

This plotting procedure provides a neater visual display of the chromosomes without marker names overlapping vertically. The plotting region will adjust itself to ensure that all marker names are in the region. For this reason the default value for the "cex" parameter passed to "text" should be manipulated until an aesthetic genetic map is reached.

For large maps with many chromosomes, marker names and adjacent chromosomes will overlap horizontally. For the interest of readability this has not been corrected. For this particular situation it is suggested that the user horizontally maximise the plotting window until no overlapping occurs or subset the chromosome to achieve the desired result.

Value

This invisibly returns the following list for manipulation with link.map.wgaim

mt A list named by the chromosomes with each element containing the locations of the marker names after correcting for overlapping
map A list named by the chromosomes with each element containing the locations of markers on the chromosomes
chrpos The numerical position of the chromosomes on the plotting region

Author(s)

Julian Taylor

See Also

link.map.wgaim

Examples


data(raccas, package = "wgaim")
link.map(raccas, cex = 0.5) 


[Package wgaim version 0.2 Index]