link.map.default {wgaim}R Documentation

Plot a genetic linkage map with QTL's for multiple traits

Description

Neatly plots the genetic linkage map with marker locations, marker names and highlights QTL's with their associated flanking markers for multiple traits obtained from a list of wgaim fits.

Usage

## Default S3 method:
link.map(object, parentData, chr, max.dist, marker.names = TRUE, 
    clist = list(qcol = rainbow(length(object)), mcol = "red", 
        tcol = rainbow(length(object))), trait.labels = NULL, tick = FALSE, ...)

Arguments

object a list object with elements inheriting the 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 colors used to highlight the QTL regions and their flanking markers. qcol is the colors of the QTL regions (defaults to rainbow(n) where n is the length of object). mcol is the color the flanking markers. tcol is the color of the trait names used in each model (defaults to the same color as the QTL regions). See par for color options
trait.labels character string naming the trait used in the model object, defaults to the names of the traits used in each model.
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 is a wrapper for link.map.wgaim and displays QTLs for multiple traits obtained from a list of models given by object. Alternative labels for the traits can be given, in model order, using trait.labels.

Color specific highligting of the QTLs is also available using clist. This differs slightly from link.map.wgaim. Here the qcol and tcol should be given a set of colors equal to the length of object. Let n be the length of object. Then if qcol is NULL or length of qcol is not equal to n then it defaults to rainbow(n). If tcol is NULL or length of tcol is not equal to n or 1 then it defaults to the colors of qcol. Examples of different color combinations are given below.

Value

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

Author(s)

Julian Taylor

See Also

link.map.cross, link.map.wgaim

Examples


## Not run: 
## fit wgaim models

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

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

## plot QTL intervals

# matching rainbow QTL color and trait names, red flanking markers
# (default) and gray background markers.

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

# rainbow QTL color and black trait names, red flanking markers
# (default) and gray background markers.

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

# monochromatic plot: gray QTLs, black trait names, black flanking
# markers and gray background markers

link.map(list(zn.qtl,zn.qtlS), raccasM, cex = 0.6, clist(qcol =
rep(gray(0.8), 2), tcol = "black", mcol = "black"), col = "gray")

## End(Not run)

[Package wgaim version 0.2 Index]