[R] Solved: Help plotting some data

[Gavin Simpson]

Hi!

The other day I asked a couple of questions about plotting some data.

Firstly I wanted to specify the colours used for the text plotted using:
> text(chem.predict[,1:2], labels = km$cluster)

Matt Wiener suggested:
> col.vec <- c("black", "red", "blue")
> text(chem.predict[,1:2], labels = km$cluster, color =
col.vec[km$clusters])

Cheers Matt, that worked great.

Secondly I wanted to know how to plot just the loadings of a PCA as
biplot arrows, i.e. plot a biplot but without plotting the labels for
the scores.

I solved this by taking the biplot.default code and adding an option
pscores to the call.  This is FALSE by default.  I then put an if clause
before the bit of the code that plots the labels for the PCA scores, so
that they only get plotted if you specify pscores=TRUE.  My function for
doing this is copied below, with a couple of extra modifications so that
I can get the plot as I required.

Cheers for the help, and for such an excellent piece of software.  I'm a
R newbie and am constantly surprised how easy it is get R to do the
things you want to do with it.

Gav

my.biplot <- function (x, y, var.axes = TRUE, col, cex = c(1, 0.4), 
    xlabs = NULL, ylabs = NULL, expand = 1, xlim = NULL, ylim = NULL,
arrow.len = 0.1, 
    pscores = FALSE, xlab="", ylab="", ...) 
{
    labx <- xlab
    laby <- ylab
    n <- nrow(x)
    p <- nrow(y)
    if (missing(xlabs)) {
        xlabs <- dimnames(x)[[1]]
        if (is.null(xlabs)) 
            xlabs <- 1:n
    }
    xlabs <- as.character(xlabs)
    dimnames(x) <- list(xlabs, dimnames(x)[[2]])
    if (missing(ylabs)) {
        ylabs <- dimnames(y)[[1]]
        if (is.null(ylabs)) 
            ylabs <- paste("Var", 1:p)
    }
    ylabs <- as.character(ylabs)
    dimnames(y) <- list(ylabs, dimnames(y)[[2]])
    if (length(cex) == 1) 
        cex <- c(cex, cex)
    if (missing(col)) {
        col <- par("col")
        if (!is.numeric(col)) 
            col <- match(col, palette())
        col <- c(col, col + 1)
    }
    else if (length(col) == 1) 
        col <- c(col, col)
    unsigned.range <- function(x) c(-abs(min(x)), abs(max(x)))
    rangx1 <- unsigned.range(x[, 1])
    rangx2 <- unsigned.range(x[, 2])
    rangy1 <- unsigned.range(y[, 1])
    rangy2 <- unsigned.range(y[, 2])
    if (missing(xlim) && missing(ylim)) 
        xlim <- ylim <- rangx1 <- rangx2 <- range(rangx1, rangx2)
    else if (missing(xlim)) 
        xlim <- rangx1
    else ylim <- rangx2
    ratio <- max(rangy1/rangx1, rangy2/rangx2)/expand
    on.exit(par(oldpar))
    oldpar <- par(pty = "s")
    plot(x, type = "n", xlim = xlim, ylim = ylim, col = col[1],
xlab=labx, ylab=laby, ...)
    if (pscores)	
    	text(x, xlabs, cex = cex[1], col = col[1], ...)
    par(new = TRUE)
    plot(y, axes = FALSE, type = "n", xlim = xlim * ratio, ylim = ylim *

        ratio, xlab = "", ylab = "", col = col[1], ...)
    axis(3, col = col[2])
    axis(4, col = col[2])
    box(col = col[1])
    text(y, labels = ylabs, cex = cex[2], col = col[2], ...)
    if (var.axes) 
        arrows(0, 0, y[, 1] * 0.8, y[, 2] * 0.8, col = col[2], 
            length = arrow.len)
    invisible()
}

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