dlmap.link.plot {dlmap} | R Documentation |
Plots the genetic linkage map for a selection of chromosomes. Indicates marker
locations, marker names, and detected QTL positions and associated flanking
markers obtained from a dlmap
fit.
dlmap.link.plot(output, chr, max.dist, marker.names=TRUE, qcol="light blue", mcol="red", pcol="purple", ...) link.map.cross(object, chr, max.dist, marker.names = TRUE, horizontal = FALSE, ...)
output |
object of class dlmap |
object |
object of class cross |
chr |
character string naming the subset of chromosomes to plot; or, if numeric, a vector of chromosome indices |
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 |
colour of intervals surrounding QTL (see par for colour options) |
mcol |
colour of QTL flanking markers (see par for colour options) |
pcol |
colour of QTL positions (see par for colour options) |
horizontal |
logical value. If TRUE then map is plotted horizontally. Defaults to FALSE |
... |
arguments passed to "plot" to set up the plot region. Arguments may also be passed to "text" for the manipulation of the marker names |
The function link.map.cross
was written by Julian Taylor for the
wgaim
package and is built upon here by adding QTL regions and estimated
positions to the map.
The function dlmap.plot.map
provides a neat visual display of
chromosomes. If no QTL are detected, only the linkage map will be plotted;
otherwise detected QTL will be placed at their estimated positions
and the intervals around them (and flanking markers) will be highlighted.
If a subset of chromosomes are plotted and detected QTLs exist outside that
subset a warning will be given that QTLs have been omitted from the display.
The arguments mcol
, qcol
and pcol
have been addedd for
personal colour highlighting the flanking markers, QTL regions and QTL
positions respectively. The procedure may also be given the usual col
argument which will be passed on to the other markers.
In order to ensure that all marker names are displayed without vertical overlap, the default value of the "cex" parameter passed to "text" should be mainpulated. For large maps with many chromosomes, marker names and adjacent chromosomes will overlap horizontally. In this case it is suggested that the user horizontally maximize the plotting window to remove overlap, or subset the chromosomes displayed.
The genetic linkage map is plotted with shaded QTL regions, marked estimated positions, and highlighted flanking markers.
Emma Huang and Andrew George; Julian Taylor
Huang, BE and George, AW. Look before you leap: A new approach to QTL mapping. submitted to Genetics
# load dataset data(BSdat) ## Not run: dlmap.convert.cross(format="rqtl", obj=BSdat) BSdl <- dlmap.asreml(phename="phenotype", estmap=FALSE, filestem="BS") dlmap.link.map(BSdl) ## End(Not run)