wgaim (version 2.0-1)

linkMap.default: Plot a genetic linkage map with QTL for multiple traits

Description

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

Usage

# S3 method for default
linkMap(object, intervalObj, chr, chr.dist, marker.names
    = "markers", flanking = TRUE, list.col = list(q.col = rainbow(length(object)),
    m.col = "red", t.col = rainbow(length(object))), list.cex =
    list(m.cex = 0.6, t.cex = 0.6), trait.labels = NULL, tick = FALSE, ...)

Value

For a set of "interval" analyses, the genetic linkage map is plotted with shaded QTL regions and highlighted flanking markers. For a set of "marker" analyses, symbols are placed at the QTL locations and the markers are highlighted.

Arguments

object

a list object with elements inheriting the class "wgaim"

intervalObj

object of class "cross" or "interval"

chr

character string naming the subset of chromosomes to plot

chr.dist

a list containing named elements "start" and "end" containing the start and end distances in cM the genetic map should be subsetted by. Each of these may also be a vector of distances equal to the length of the number of linkage groups to be plotted.

marker.names

a character string naming the type of marker information to plot. If "dist" then distances are plotted alongside each chromosome on the left. If "markers" then marker names are plotted instead. Defaults to "markers".

flanking

logical value. If TRUE then only plot marker names or distances for flanking markers of the QTL. Defaults to TRUE

list.col

named list of colors used to highlight the QTL regions and their flanking markers. q.col is the colors of the QTL regions (defaults to rainbow(n) where n is the length of object). m.col is the color the flanking markers. t.col 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

list.cex

a named list object containing the character expansion factors for the marker names m.cex and the trait labels t.cex

trait.labels

character string naming the trait used in the model object, defaults to the response names extracted from the fixed compoenent of the base model.

tick

logical value. If TRUE then an axis with tick marks are generated for the chromosome names

...

arguments passed to the plot() function to set up the plot region. Arguments may also be passed to the text() function for the manipulation of the marker names

Author

Julian Taylor

Details

This plotting procedure is a wrapper for linkMap.wgaim and displays QTL 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 QTL is also available using clist. This differs slightly from linkMap.wgaim. Here the q.col and t.col should be given a set of colors equal to the length of object. Let n be the length of object. Then if q.col is NULL or length of q.col is not equal to n then it defaults to rainbow(n). If t.col is NULL or length of t.col is not equal to n or 1 then it defaults to the colors of q.col. Examples of different color combinations are given below in the examples.

The list.cex argument can be used to manipulate the character expansion of the marker names using m.cex or the character expansion of the trait.labels using t.cex. If a set of "marker" analyses has been performed then pch is used to plot a symbol at the location of the QTL. This character can be changed using the usual arguments such as pch or cex that are passed through the ... argument.

References

Verbyla, A. P & Taylor, J. D, Verbyla, K. L (2012). RWGAIM: An efficient high dimensional random whole genome average (QTL) interval mapping approach. Genetics Research. 94, 291-306.

Julian Taylor, Arunas Vebyla (2011). R Package wgaim: QTL Analysis in Bi-Parental Populations Using Linear Mixed Models. Journal of Statistical Software, 40(7), 1-18. URL http://www.jstatsoft.org/v40/i07/.

Verbyla, A. P., Cullis, B. R., Thompson, R (2007) The analysis of QTL by simultaneous use of the full linkage map. Theoretical and Applied Genetics, 116, 95-111.

See Also

linkMap.cross, linkMap.wgaim

Examples

if (FALSE) {
## fit wgaim models

rktgw.qtl <- wgaim(rktgw.asf, intervalObj = genoRxK, merge.by = "Genotype",
                 trace = "trace.txt", na.action = na.method(x = "include"))

rkyld.qtl <- wgaim(rkyld.asf, intervalObj = genoRxK, merge.by = "Genotype",
                 trace = "trace.txt", na.action = na.method(x = "include"))

## plot QTL intervals

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

linkMap(list(rktgw.qtl,rkyld.qtl), genoRxK, col = "gray")

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

linkMap(list(rktgw.qtl,rkyld.qtl), genoRxK, list.col = list(t.col =
"black", m.col = "red"), col = "gray")

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

linkMap(list(rktgw.qtl,rkyld.qtl), genoRxK, list.col = list(q.col =
rep(gray(0.8), 2), t.col = "black", mcol = "black"), col = "gray")

}