qtl (version 1.70)

plotMap: Plot genetic map

Description

Plot genetic map of marker locations for all chromosomes.

Usage

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

Value

None.

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 (and names) of chromosomes. 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.

Author

Karl W Broman,

Details

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

For a comparison of two maps, the first map is on the left (or, if horizontal=TRUE, on the top). Lines are drawn to connect markers. Markers that exist in just one map and not the other are indicated by short line segments, on one side or the other, that are not connected across.

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.

See Also

est.map, plot.cross

Examples

data(fake.bc)
fake.bc <- subset(fake.bc, chr=18:19)
plotMap(fake.bc)
plotMap(fake.bc,horizontal=TRUE)

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

plotMap(fake.bc, show.marker.names=TRUE)