linkMap.cross {wgaim} | R Documentation |
Plot a genetic linkage map
Description
Neatly plots the genetic linkage map with marker locations and marker names.
Usage
## S3 method for class 'cross'
linkMap(object, chr, chr.dist, marker.names = "markers",
tick = FALSE, squash = TRUE, m.cex = 0.6, ...)
Arguments
object |
object of class |
chr |
character string naming the subset of chromosomes to plot |
chr.dist |
a list containing named elements |
marker.names |
a character string naming the type of marker
information to plot. If |
tick |
logical value. If |
squash |
logical value. if |
m.cex |
the expansion factor to use for the marker names |
... |
arguments passed to |
Details
This plotting procedure provides a visual display of the
chromosomes without marker names overlapping vertically. The plotting
region will adjust itself to ensure that all marker names are in the region. For
this reason the value for "m.cex"
is passed to the text()
function and should be manipulated until an aesthetic genetic map is reached.
For large maps with many chromosomes, marker names and adjacent chromosomes will overlap horizontally. For the interest of readability this has not been corrected. For this particular situation it is suggested that the user horizontally maximise the plotting window until no overlapping occurs or subset the genetic map to achieve the desired result.
Value
This invisibly returns the following list for manipulation with
linkMap.wgaim()
mt |
A list named by the chromosomes with each element containing the locations of the marker names after correcting for overlapping |
map |
A list named by the chromosomes with each element containing the locations of markers on the chromosomes |
chrpos |
The numerical position of the chromosomes on the plotting region |
Author(s)
Julian Taylor
References
Verbyla, A. P & Taylor, J. D, Verbyla, K. L (2012). RWGAIM: An efficient high dimensional random whole genome average (QTL) interval mapping approach. Genetics Research. 94, 291-306.
Julian Taylor, Arunas Vebyla (2011). R Package wgaim: QTL Analysis in Bi-Parental Populations Using Linear Mixed Models. Journal of Statistical Software, 40(7), 1-18. URL http://www.jstatsoft.org/v40/i07/.
Verbyla, A. P., Cullis, B. R., Thompson, R (2007) The analysis of QTL by simultaneous use of the full linkage map. Theoretical and Applied Genetics, 116, 95-111.
See Also
Examples
data(genoSxT, package = "wgaim")
## plot linkage map with marker names
linkMap(genoSxT, cex = 0.5)
## plot linkage map with distances
linkMap(genoSxT, cex = 0.5, marker.names = "dist")