Nothing
plot.grpreg <- function(x, alpha=1, legend.loc, label=FALSE, log.l=FALSE, norm=FALSE, ...) {
if (norm) {
Y <- predict(x, type="norm")
if (any(x$group==0)) Y <- Y[-1,]
nonzero <- which(apply(abs(Y), 1, sum)!=0)
Y <- Y[nonzero,]
g <- 1:nrow(Y)
} else {
if (length(dim(x$beta))==3) {
beta <- matrix(x$beta[, -1, , drop=FALSE], ncol=dim(x$beta)[3])
} else if (inherits(x, "grpsurv")) {
beta <- x$beta
} else {
beta <- x$beta[-1, , drop=FALSE]
}
penalized <- which(x$group!=0)
nonzero <- which(apply(abs(beta), 1, sum)!=0)
ind <- intersect(penalized, nonzero)
Y <- beta[ind, , drop=FALSE]
g <- as.integer(as.factor(x$group[ind]))
}
p <- nrow(Y)
l <- x$lambda
n.g <- max(g)
if (log.l) {
l <- log(l)
xlab <- expression(log(lambda))
} else xlab <- expression(lambda)
plot.args <- list(x=l, y=1:length(l), ylim=range(Y), xlab=xlab, ylab="", type="n", xlim=rev(range(l)), las=1, bty="n")
new.args <- list(...)
if (length(new.args)) {
new.plot.args <- new.args[names(new.args) %in% c(names(par()), names(formals(plot.default)))]
plot.args[names(new.plot.args)] <- new.plot.args
}
do.call("plot", plot.args)
if (plot.args$ylab=="") {
ylab <- if (norm) expression("||"*hat(beta)*"||") else expression(hat(beta))
mtext(ylab, 2, 3.5, las=1, adj=0)
}
abline(h=0, lwd=0.5, col="gray")
cols <- hcl(h=seq(15, 375, len=max(4, n.g+1)), l=60, c=150, alpha=alpha)
cols <- if (n.g==2) cols[c(1,3)] else cols[1:n.g]
line.args <- list(col=cols, lwd=1+2*exp(-p/20), lty=1, pch="")
if (length(new.args)) line.args[names(new.args)] <- new.args
line.args$x <- l
line.args$y <- t(Y)
line.args$col <- line.args$col[g]
line.args$lty <- rep(line.args$lty, length.out=max(g))
line.args$lty <- line.args$lty[g]
do.call("matlines", line.args)
if(!missing(legend.loc)) {
legend.args <- list(col=cols, lwd=line.args$lwd, lty=line.args$lty, legend=names(x$group.multiplier))
if (length(new.args)) {
new.legend.args <- new.args[names(new.args) %in% names(formals(legend))]
legend.args[names(new.legend.args)] <- new.legend.args
}
legend.args$x <- legend.loc
do.call("legend", legend.args)
}
if (label) {
ypos <- Y[, ncol(Y)]
text(-0.001, ypos, names(ypos), xpd=NA, adj=c(0, NA))
}
}
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