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, qcol = "light blue", mcol = "red", ...)
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 |
qcol |
color of QTL regions (see par for colour options) |
mcol |
color of QTL flanking markers (see par for colour options) |
... |
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 arguments mcol
and qcol
have been added for personal
colour highlighting of the QTL regions and flanking markers. For greater
flexibility the procedure may also be given the usual col
argument that will be passed to the other markers.
At the current stage the plotting of the linkage map only occurs horizontally.
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, mcol = "red", col = "blue") ## End(Not run)