link.map.wgaim {wgaim} | R Documentation |
Neatly plots the genetic linkage map with marker locations,
marker names and highlights QTL's with their associated flanking markers
obtained from a fit to wgaim
.
## S3 method for class 'wgaim': link.map(object, parentData, chr, max.dist, marker.names = TRUE, clist = list(qcol = "light blue", mcol = "red", tcol = "light blue"), trait.labels = NULL, tick = FALSE, ...)
object |
object of 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 colours used to highlight the QTL regions and
their flanking markers. qcol is the color of the QTL
regions. mcol is the color the flanking markers. tcol
is the color of the trait name used in the model object (see par for colour options) |
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 "plot " to set up the plot
region. Arguments may also be passed to "text " for the
manipulation of the marker names |
This plotting procedure builds on link.map.cross
by adding the
QTL regions to the map and highlighting the flanking 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's have been omitted from the display.
The codeList
arguments qcol
, mcol
and tcol
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 genetic linkage map is plotted with shaded QTL regions and highlighted flanking markers.
Julian Taylor
## Not run: # fit wgaim model zn.qtl <- wgaim(zn.fm, parentData = raccasM, trace = "trace.txt", na.method.X = "include") # plot QTL intervals link.map(zn.qtl, raccasM, cex = 0.6, clist = list(mcol = "red"), col = "gray") ## End(Not run)