link.map.default {wgaim} | R Documentation |
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.
## 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, ...)
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 |
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.
The genetic linkage map is plotted with shaded QTL regions and highlighted flanking markers.
Julian Taylor
link.map.cross
, link.map.wgaim
## 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)