bqtl (version 1.0-38)

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 map.frame
plot(x, y, fun = if (y.type == "matrix") matlines else
                 lines, type = "l", include.rug = TRUE, rug.lwd = 0.1,
                 title.string = NULL, y.range = NULL, ylab =
                 deparse(substitute(y)), xlab = "Location", ...)

Value

NULL - this function is called only for its side effects

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 markers and virtual markers (if any).

...

more args

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 plot.

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

rug.lwd

size of ticks

title.string

(optional) label to prepend to each title

y.range

range for y limits

ylab

plot label for y-axis, see par

xlab

plot label for x-axis, see par

Author

Charles C. Berry

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)
 rm(null.llk, llk, little.ana.bc, .old.par )