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###########################################################################
## ##
## minDC & methods - function to extract minimum DC values from objects ##
## and assocaited methods ##
## ##
## Created : 12-Feb-2007 ##
## Author : Gavin Simpson ##
## Version : 0.0-1 ##
## Last modified : 12-Feb-2007 ##
## ##
###########################################################################
minDC <- function(x, ...) UseMethod("minDC")
minDC.default <- function(x, ...) {
if(is.null(x$minDC))
stop("No 'minDC' component of 'x' found.")
res <- list(minDC = x$minDC)
class(res) <- "minDC"
return(res)
}
minDC.predict.mat <- function(x, ...) {
if(is.null(x$minDC))
stop("'minDC' is not currently available for all\n'predict.mat' options.")
res <- list(minDC = x$minDC, method = x$method, quantiles = x$quantiles)
class(res) <- "minDC"
return(res)
}
minDC.analog <- function(x, probs = c(0.01, 0.02, 0.05, 0.1),
...) {
if(class(x) != "analog")
stop("'x' is not of class \"analog\".")
minDC <- apply(x$analogs, 2, min)
quant <- NULL
if(!is.null(x$train))
quant <- quantile(as.dist(x$train), probs = probs)
res <- list(minDC = minDC, method = x$method, quantiles = quant)
class(res) <- "minDC"
return(res)
}
print.minDC <- function(x, digits = 3, ...) {
cat("\n")
writeLines(strwrap("Minimum dissimilarity per sample", prefix = "\t"))
cat("\n")
cat(paste("Dissimilarity:", x$method, "\n\n"))
print(unclass(x$minDC), digits = digits)
}
plot.minDC <- function(x, depths, use.labels = FALSE,
quantiles = TRUE,
rev.x = TRUE,
type = "l",
xlim, ylim,
xlab = "", ylab = "Dissimilarity",
main = "",
sub = NULL,
col.quantile = "red",
lty.quantile = "dotted",
...) {
if(quantiles) {
mars <- par("mar")
opar <- par(mar = c(mars[1:3], 3.1))
on.exit(par(opar))
}
if(missing(depths))
{
if(use.labels) {
depths <- as.numeric(names(x$minDC))
} else {
stop("If \"use.labels = FALSE\", then \"depths\" must be provided.")
}
}
if(missing(xlim))
xlim <- range(depths)
if(rev.x)
xlim <- rev(xlim)
if(missing(ylim))
ylim <- range(x$minDC)
if(is.null(sub))
sub <- paste("Dissimilarity:", x$method)
plot(depths, x$minDC, ylim = ylim, xlim = xlim, type = "n",
ylab = ylab, xlab = xlab, main = main, sub = sub, ...)
if(quantiles & !is.null(x$quantile)) {
abline(h = x$quantile, lty = lty.quantile, col = col.quantile)
axis(4, at = x$quantile, labels = names(x$quantile), las = 2)
}
lines(depths, x$minDC, type = type)
invisible()
}
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