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######################################################################
# plotModel.R
#
# copyright (c) 2008-9, Karl W Broman
# last modified January, 2009
# first written Apr, 2008
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License,
# version 3, as published by the Free Software Foundation.
#
# This program is distributed in the hope that it will be useful,
# but without any warranty; without even the implied warranty of
# merchantability or fitness for a particular purpose. See the GNU
# General Public License, version 3, for more details.
#
# A copy of the GNU General Public License, version 3, is available
# at http://www.r-project.org/Licenses/GPL-3
#
# Part of the R/qtl package
# Contains: plotModel
#
######################################################################
######################################################################
# plotModel
#
# plot a QTL model
######################################################################
plotModel <-
function(qtl, formula, circrad.rel=0.25, circrad.abs,
cex.name=1, chronly=FALSE, order, ...)
{
if(missing(qtl))
stop("Must provide qtl object or a vector of QTL names")
if(is.character(qtl)) { # qtl names
if(missing(formula)) formula <- NULL
}
else {
if(missing(formula)) {
if("formula" %in% names(attributes(qtl)))
formula <- attr(qtl, "formula")
else {
if("formula" %in% names(qtl))
formula <- qtl$formula
else formula <- NULL
}
}
if(length(qtl)>0) {
if(chronly) qtl <- qtl$chr
else {
if("name" %in% names(qtl))
qtl <- qtl$name
else {
if("pos" %in% names(qtl))
qtl <- paste(qtl$chr, roundqtlpos(qtl$pos, 1), sep="@")
else qtl <- qtl$chr
}
}
}
}
nqtl <- length(qtl)
if(!is.null(formula)) {
if(is.character(formula))
formula <- as.formula(formula)
theterms <- attr(terms(formula), "factors")[-1,]
rn <- rownames(theterms)
g <- grep("^[Qq][0-9]+$", rn)
qtlnum <- as.numeric(substr(rn[g], 2, nchar(rn[g])))
if(any(qtlnum < 1 | qtlnum > nqtl))
stop("QTL in formula must be numbered between 1 and ", nqtl)
cn <- colnames(theterms)
intxn <- cn[grep("^[Qq][0-9]+:[Qq][0-9]+$", cn)]
}
else intxn <- NULL
plot(0,0,type="n", xlab="", ylab="", xaxt="n", yaxt="n",
xaxs="i", yaxs="i", xlim=c(-1.5,1.5), ylim=c(-1.5,1.5),
...)
if(!is.null(qtl) && length(qtl) > 0) {
radloc <- rev(seq(pi/2, 2.5*pi, len=nqtl+1)[-1])
xloc <- cos(radloc)
yloc <- sin(radloc)
rad <- seq(0, 2*pi, length=100)
if(missing(circrad.abs)) {
if(length(xloc) == 1)
circrad.abs <- circrad.rel*2
else
circrad.abs <- circrad.rel * sqrt(diff(xloc[1:2])^2 + diff(yloc[1:2])^2)
if(circrad.abs > 0.45) circrad.abs <- 0.45
}
# use the smallest of the two relative lengths
u <- par("usr")
pin <- par("pin")
pin <- pin/c(diff(u[1:2]), diff(u[3:4]))
circrad.abs<- circrad.abs/(pin/min(pin))
if(!missing(order)) {
if(length(order) != length(qtl))
stop("order should have length ", nqtl)
if(!all(sort(order) == seq(along=qtl)))
stop("order should be a permutaton of 1,2,...,", nqtl)
xloc <- xloc[order(order)]
yloc <- yloc[order(order)]
}
if(length(intxn) > 0) {
for(i in intxn) {
thisint <- strsplit(i, ":")[[1]]
theseqtl <- as.numeric(substr(thisint, 2, nchar(thisint)))
lines(xloc[theseqtl], yloc[theseqtl], lwd=2)
}
}
for(i in seq(along=xloc))
polygon(xloc[i]+cos(rad)*circrad.abs[1], yloc[i]+sin(rad)*circrad.abs[2], col="white", border="black", lwd=2)
text(xloc, yloc, qtl, cex=cex.name)
}
invisible()
}
roundqtlpos <-
function (x, digits = 1)
{
if (digits < 1)
stop("This is intended for the case digits >= 1.")
y <- as.character(round(x, digits))
z <- strsplit(y, "\\.")
sapply(z, function(a, digits) {
if (length(a) == 1)
b <- paste(a[1], ".", paste(rep("0", digits), collapse = ""),
sep = "")
else {
if (nchar(a[2]) == digits)
b <- paste(a, collapse = ".")
else b <- paste(a[1], ".", a[2], paste(rep("0", digits -
nchar(a[2])), collapse = "."), sep = "")
}
}, digits)
}
# end of plotModel.R
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