plot.map {qtl}R Documentation

Plot genetic map

Description

Plot genetic map of marker locations for all chromosomes.

Usage

## S3 method for class 'map':
plot(x, map2, chr, horizontal=FALSE, shift=TRUE,
     show.marker.names=FALSE, alternate.chrid=FALSE, ...)

Arguments

x A list whose components are vectors of marker locations. A cross object may be given instead, in which case the genetic map it contains is used.
map2 An optional second genetic map with the same number of chromosomes and markers as the first. As with the first argument, a cross object may be given instead. If this argument is given, a comparison of the two genetic maps is plotted.
chr Optional vector indicating the chromosomes to plot. This should be a vector of character strings referring to chromosomes by name; numeric values are converted to strings. Refer to chromosomes with a preceding - to have all chromosomes but those considered. A logical (TRUE/FALSE) vector may also be used.
horizontal Specifies whether the chromosomes should be plotted horizontally.
shift If TRUE, shift the first marker on each chromosome to be at 0 cM.
show.marker.names If TRUE, marker names are included.
alternate.chrid If TRUE and more than one chromosome is plotted, alternate the placement of chromosome axis labels, so that they may be more easily distinguished.
... Passed to plot.

Details

Plots the genetic map for each chromosome, or a comparison of the genetic maps if two maps are given.

For a sex-specific map, female and male maps are plotted against one another. For two sex-specific maps, the two female maps are plotted against one another and the two male maps are plotted against one another.

Value

None.

Author(s)

Karl W Broman, kbroman@biostat.wisc.edu

See Also

est.map, plot.cross

Examples

data(fake.bc)

plot.map(fake.bc)
plot.map(fake.bc,horizontal=TRUE)

newmap <- est.map(fake.bc)
plot(newmap)
plot.map(fake.bc, newmap)

plot.map(fake.bc, show.marker.names=TRUE)
[Package qtl version 1.11-12 Index]