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#$Author: sinnwell $
#$Date: 2006/05/05 20:25:12 $
#$Header: /people/biostat3/sinnwell/Projects/IBDReg/Make/RCS/plot.linkage.tests.q,v 1.3 2006/05/05 20:25:12 sinnwell Exp $
#$Locker: $
#$Log: plot.linkage.tests.q,v $
#Revision 1.3 2006/05/05 20:25:12 sinnwell
#add lwd and more types
#
#Revision 1.2 2006/05/02 16:31:42 sinnwell
#remove model-var test with covariates, commented
#
#Revision 1.1 2006/03/08 16:34:12 sinnwell
#Initial revision
#
##################################
# Jason Sinnwell
# Daniel Schaid
# Mayo Clinic, HSR, Biostatistics
# 2005
##################################
plot.linkage.tests <- function(x, ...) {
if(!inherits(x, "linkage.tests"))
stop("Not a linkage.tests object")
xpos <- x$linkage.frame$positions
linkage.only <- x$ncov==1
# pull off title parm from ellipsis, eg. an extra label for chrom, etc
dots <- as.list(substitute(list(...)))[-1]
title.indx <- match('title', names(dots))
title.user <- if(!is.na(title.indx)) dots[title.indx]$title else NULL
if(linkage.only) {
minp <- min(c(.001, # corresponds to upper ylim=3
x$linkage.cons.frame$pval.linkage.cons))
title.txt <- paste(x$status.method, "PAIRS: Linkage Test")
plotpval(pos=xpos, pmat=x$linkage.cons.frame$pval.linkage.cons,
lty=1, col=1,lwd=2,
title=paste(title.user, "\n", x$status.method,
"PAIRS: Constrained Linkage Test", sep=" "))
} else {
plotpval(pos=xpos,
pmat=cbind(x$linkage.cons.frame$pval.linkage.cons,
x$linkcov.cons.frame$pval.linkcov.cons,
#x$cov.model.cons.frame$pval.cov.model,
x$cov.robust.cons.frame$pval.cov.robust),
lty=c(1,3,6), col=c(1,2,4), lwd=c(2,3,2), #lty=c(1,3,5,6), col=1:4,
title=paste(title.user, "\n", x$status.method,
"PAIRS: Constrained Linkage Tests with Covariates"),
legend=c("Linkage without Covariates",
"Linkage with Covariates",
#"Covariate Eff, model-var",
"Covariate Eff, robust-var"))
}
invisible(x)
}
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