linkMap.cross: Plot a genetic linkage map
In wgaim: Whole Genome Average Interval Mapping for QTL Detection and Estimation using ASReml-R

linkMap.cross

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 `"cross"`
`chr`	character string naming the subset of chromosomes to plot
`chr.dist`	a list containing named elements `"start"` and `"end"` containing the start and end distances in cM the genetic map should be subsetted by. Each of these may also be a vector of distances equal to the length of the number of linkage groups to be plotted.
`marker.names`	a character string naming the type of marker information to plot. If `"dist"` then distances are plotted alongside each chromosome on the left. If `"markers"` then marker names are plotted instead. Defaults to `"markers"`
`tick`	logical value. If `TRUE` then an axis with tick marks are generated for the chromosome names. Defaults to `FALSE`
`squash`	logical value. if `TRUE` then creates extra room on the left side of the chromosomes. This is useful for plotting trait names for QTL using `linkMap.wgaim()` and `linkMap.default()`
`m.cex`	the expansion factor to use for the marker names
`...`	arguments passed to `plot()` function to set up the plot region. Arguments may also be passed to `text()` function for the manipulation of the marker names

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 https://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.

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")

wgaim documentation built on Sept. 11, 2024, 9:31 p.m.