Neatly plots the genetic linkage map with marker locations,
marker names and highlights QTL with their associated flanking markers
obtained from a wgaim model.
# S3 method for 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, ...)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.
object of class "wgaim"
object of class "cross" or "interval"
character string naming the subset of chromosomes to plot
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.
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".
logical value. If TRUE then only plot marker
names or distances for flanking markers of the QTL. Defualts to TRUE
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)
a named list object containing the character expansion
factors for the marker names m.cex and the trait labels t.cex
character string naming the trait used in the model object
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
Julian Taylor
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.
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 https://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.
linkMap.cross, wgaim
if (FALSE) {
# 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")
}
Run the code above in your browser using DataLab