linkMap.wgaim {wgaim}

Plot a genetic linkage map with QTL

Description

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

Usage

## S3 method for class 'wgaim'
linkMap(object, intervalObj, chr, chr.dist,
    marker.names = "markers", flanking = TRUE, list.col = list(q.col = "light blue",
    m.col = "red", t.col = "light blue"), list.cex = list(t.cex = 0.6,
    m.cex = 0.6), trait.labels = NULL, tick = FALSE, ...)

Arguments

object

object of 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 names 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. Defualts to TRUE

list.col

named list of colours used to highlight the QTL regions and their flanking markers. q.col is the color of the QTL regions. m.col is the color the flanking markers. t.col is the color of the trait name used in the model object (see par for colour 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

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 and plot any symbols if required

Details

This plotting procedure builds on linkMap.cross() by adding the QTL regions to the map and highlighting the appropriate 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 have been omitted from the display.

The list.col arguments q.col, m.col and t.col 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.

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 "marker" analysis 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.

Value

For an "interval" analysis, the genetic linkage map is plotted with shaded QTL regions and highlighted flanking markers. For a "marker" analysis, a symbol is placed at the QTL locations and the markers are highlighted.

Author(s)

Julian Taylor

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, wgaim

Examples

## Not run: 
# fit wgaim model

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

# plot QTL

linkMap(yield.qtl, genoRxK, list.col = list(m.col = "red"), col = "gray")


## End(Not run)