bqtl (version 1.0-5)

plot.map.frame: plots by chromosome location

Description

Multiple x-y plots are formed using chromosome numbers (chr.num) and positions (pos.plot) specified in a object of the sort created by make.map.frame

Usage

## S3 method for class 'map.frame':
plot(x, ...)

Arguments

x

A map.frame.object or an analysis.object

y

(optional) A vector with as many elements or a matrix with as many rows as nrow(x) . If omitted, a plot will be drawn in a single frame representing the chromosomes as horizontal bars and giving tic marks to show the locations marke

fun

A plotting function to be used after the plot axes and labels have been drawn. The current default if (y.type == "matrix") matlines else lines usually is good enough. But a fancier function could be used for a fancier pl

type

"l" for lines, "p" for points, et cetera. see par

include.rug

if TRUE place a tick on the x-axis at each marker location

title.string

(optional) label to prepend to each title

ylab

plot label for y-axis, see par

xlab

plot label for x-axis, see par

...

(optional args to pass to fun

Value

• NULL - this function is called only for its side effects

synopsis

plot.map.frame(x, y, fun, type, include.rug, rug.lwd, title.string, y.range, ylab, xlab, ...)

Details

This function enables drawing graphs that depend on chromosome and chromosome location. Typically, one will use a command like par(mfrow=c(nrows,ncols)) first to set up a page on which multiple plots will be drawn. However, one can draw one plot per page on postscript devices by leaving par(mfrow=c(1,1))

See Also

plot, lines, and matlines for general information on plotting functions; par for optional arguments to add as arguments; and make.map.frame for the details on the object the drives this function.

Examples

data( little.ana.bc )
null.llk <- loglik(bqtl(bc.phenotype~1,little.ana.bc))
llk <- loglik( bqtl( bc.phenotype~locus(all), little.ana.bc) ) - null.llk
.old.par <- par(mfrow=c(2,3))
plot.map.frame(little.ana.bc$map.frame,llk)
par(.old.par)
<testonly>rm(null.llk, llk, little.ana.bc, .old.par )</testonly>