link.map.wgaim {wgaim}R Documentation

Plot a genetic linkage map with QTL's

Description

Neatly plots the genetic linkage map with marker locations, marker names and highlights QTL's with their associated flanking markers obtained from a fit to wgaim.

Usage

## S3 method for class 'wgaim':
link.map(object, parentData, chr, max.dist, marker.names = TRUE,
clist = list(qcol = "light blue", mcol = "red", tcol = "light blue"),
trait.labels = NULL, tick = FALSE, ...)

Arguments

object object of class "wgaim"
parentData 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
clist named list of colours used to highlight the QTL regions and their flanking markers. qcol is the color of the QTL regions. mcol is the color the flanking markers. tcol is the color of the trait name used in the model object (see par for colour options)
trait.labels character string naming the trait used in the model object
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 builds on link.map.cross by adding the QTL regions to the map and highlighting the flanking markers obtained from a fit to wgaim. If the linkage map is subsetted and QTL regions fall outside the remaining map a warning will be given that the QTL's have been omitted from the display.

The codeList arguments qcol, mcol and tcol have been added for personal colour highlighting of the QTL regions, flanking markers and trait names. For greater flexibility the procedure may also be given the usual col argument that will be passed to the other markers.

Value

The genetic linkage map is plotted with shaded QTL regions and highlighted flanking markers.

Author(s)

Julian Taylor

See Also

link.map.cross, wgaim

Examples


## Not run: 
# fit wgaim model

zn.qtl <- wgaim(zn.fm, parentData = raccasM, trace = "trace.txt",
na.method.X = "include")

# plot QTL intervals

link.map(zn.qtl, raccasM, cex = 0.6, clist = list(mcol = "red"), col = "gray")

## End(Not run)

[Package wgaim version 0.2 Index]