dlmap.link.plot {dlmap}R Documentation

Plot linkage map with detected QTL

Description

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.

Usage

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,  ...) 

Arguments

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

Details

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.

Value

The genetic linkage map is plotted with shaded QTL regions, marked estimated positions, and highlighted flanking markers.

Author(s)

Emma Huang and Andrew George; Julian Taylor

References

Huang, BE and George, AW. Look before you leap: A new approach to QTL mapping. submitted to Genetics

See Also

link.map

Examples

# 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)

[Package dlmap version 1.0 Index]