linkMap.default {wgaim} | R Documentation |
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
## Default S3 method:
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, ...)
Arguments
object |
a list object with elements inheriting the class |
intervalObj |
object of class |
chr |
character string naming the subset of chromosomes to plot |
chr.dist |
a list containing named elements |
marker.names |
a character string naming the type of marker
information to plot. If |
flanking |
logical value. If |
list.col |
named list of colors used to highlight the QTL regions and
their flanking markers. |
list.cex |
a named list object containing the character expansion
factors for the marker names |
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 |
... |
arguments passed to the |
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.
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.
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
Examples
## Not run:
## 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")
## End(Not run)