| plot.map.frame {bqtl} | R Documentation |
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
plot(x, ...) plot.map.frame(mf.obj, y, fun=<<see below>>, type="l", include.rug=TRUE, title.string=NULL, ylab=deparse(substitute(y)), xlab="Location", ...)
mf.obj |
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(mf.obj) . 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). |
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 |
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 |
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))
NULL - this function is called only for its side effects
Charles C. Berry cberry@ucsd.edu
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.
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)