I am not sure what you intended by
biplotes <- function(x, ...) UseMethod("biplot")
That does nothing different from biplot(). You need to call your
modified functions 'biplotes.default' and 'biplotes.princomp' and call
those via
biplotes <- function(x, ...) UseMethod("biplotes")
Anything else depends on the scoping rules for S3 methods, and those
are too complex to rely on with multiple objects of the same name --
but if your biplot.default is visible from where biplotes is called, I
would expect it to be used.
There are good reasons why the posting guide and message footers asks
for reproducible examples -- otherwise, as here, we are left to guess.
On Mon, 2 Mar 2009, japal wrote:
japal wrote:
Hello,
Something incredible (at least for me) has happen. Yesterday night I
downloaded biplot.R to edit this function and add new features I wished.
Namely I wanted to plot points belonging to different groups using
different colors and symbols. I identified which part of the original code
I had to modify. Then, I rename biplot by biplotes and executing
biplotes(x), being x a princomp class object, the function did what I
wanted.
The problem is that today I type exactly the same (after sourcing my
script file incluiding biplotes) but biplotes(x) execute the original
biplot function. Also, if I invoke any of the new arguments I wrote in the
code then multiple warnings messages are displayed. I don't understand
what is the problem. Yesterday it works perfectly. Why R does not execute
my code and call the original biplot function?
Thanks in advance,
Javier.
Sorry, I did not show the code: (I have highlighted in bold the changes)
Highlighting does not work in plain text, all you were asked to send.
***********************************
biplotes <- function(x, ...) UseMethod("biplot")
biplot.default <-
function(x, y, color="blue", char=1, var.axes = TRUE, col, cex =
rep(par("cex"), 2),
xlabs = NULL, ylabs = NULL, expand=1, xlim = NULL, ylim = NULL,
arrow.len = 0.1,
main = NULL, sub = NULL, xlab = NULL, ylab = NULL, ...)
{
n <- nrow(x)
p <- nrow(y)
if(missing(xlabs)) {
xlabs <- dimnames(x)[[1L]]
if(is.null(xlabs)) xlabs <- 1L:n
}
xlabs <- as.character(xlabs)
dimnames(x) <- list(xlabs, dimnames(x)[[2L]])
if(missing(ylabs)) {
ylabs <- dimnames(y)[[1L]]
if(is.null(ylabs)) ylabs <- paste("Var", 1L:p)
}
ylabs <- as.character(ylabs)
dimnames(y) <- list(ylabs, dimnames(y)[[2L]])
if(length(cex) == 1L) cex <- c(cex, cex)
if(missing(col)) {
col <- par("col")
if (!is.numeric(col)) col <- match(col, palette(), nomatch=1L)
col <- c(col, col + 1L)
}
else if(length(col) == 1L) col <- c(col, col)
biplot.princomp <- function(x, choices = 1L:2, scale = 1, pc.biplot=FALSE,
...)
{
if(length(choices) != 2) stop("length of choices must be 2")
if(!length(scores <- x$scores))
stop(gettextf("object '%s' has no scores", deparse(substitute(x))),
domain = NA)
lam <- x$sdev[choices]
if(is.null(n <- x$n.obs)) n <- 1
lam <- lam * sqrt(n)
if(scale < 0 || scale > 1) warning("'scale' is outside [0, 1]")
if(scale != 0) lam <- lam^scale else lam <- 1
if(pc.biplot) lam <- lam / sqrt(n)
biplot.default(t(t(scores[, choices]) / lam),
t(t(x$loadings[, choices]) * lam), ...)
invisible()
}
unsigned.range <- function(x)
c(-abs(min(x, na.rm=TRUE)), abs(max(x, na.rm=TRUE)))
rangx1 <- unsigned.range(x[, 1L])
rangx2 <- unsigned.range(x[, 2L])
rangy1 <- unsigned.range(y[, 1L])
rangy2 <- unsigned.range(y[, 2L])
if(missing(xlim) && missing(ylim))
xlim <- ylim <- rangx1 <- rangx2 <- range(rangx1, rangx2)
else if(missing(xlim)) xlim <- rangx1
else if(missing(ylim)) ylim <- rangx2
ratio <- max(rangy1/rangx1, rangy2/rangx2)/expand
on.exit(par(op))
op <- par(pty = "s")
if(!is.null(main))
op <- c(op, par(mar = par("mar")+c(0,0,1,0)))
plot(x, type = "p", xlim = xlim, ylim = ylim,
col = color,pch=char,cex=0.75, #color, símbolo y tamaños de los puntos
xlab = xlab, ylab = ylab, sub = sub, main = main, ...)
par(new = TRUE)
plot(y, axes = FALSE, type = "n", xlim = xlim*ratio, ylim = ylim*ratio,
xlab = "", ylab = "", col = col[1L], ...)
# axis(3, col = col[2L], ...)
# axis(4, col = col[2L], ...)
# box(col = col[1L])
text(y, labels=ylabs, cex = 0.9, col = "grey32", ...)
if(var.axes)
arrows(0, 0, y[,1L] * 0.8, y[,2L] * 0.8,
col = "grey32", #Arrow color
length=0.07)
invisible()
}
*********************************
Note that the problem is solved if (after sourcing the R script incluiding
biplotes function to the current R session) I only copy-paste the
biplot.princomp function into the R console. After this, biplotes apply my
changes correctly, without invoke the original biplot function. But I think
this is only a trick and not the suitable way.
Thanks again.
--
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--
Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
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