link.map.cross {wgaim} | R Documentation |
Neatly plots the genetic linkage map with marker locations and marker names.
## S3 method for class 'cross': link.map(object, chr, max.dist, marker.names = TRUE, tick = FALSE, ...)
object |
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 |
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 provides a neater 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 default value for the "cex
" parameter passed to
"text
" 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 chromosome to achieve the desired result.
This invisibly returns the following list for manipulation with
link.map.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 |
Julian Taylor
data(raccas, package = "wgaim") link.map(raccas, cex = 0.5)