R/s.var.R

In made4: Multivariate analysis of microarray data using ADE4

"s.var" <-
function (dfxy, xax = 1, yax = 2, label = row.names(dfxy), clabel = 1, 
    pch = 20, cpoint = if (clabel == 0) 1 else 0, neig = NULL, 
    cneig = 2, xlim = NULL, ylim = NULL, grid = TRUE, addaxes = TRUE, 
    cgrid = 1, include.origin = TRUE, origin = c(0, 0), sub = "", 
    csub = 1.25, possub = "bottomleft", pixmap = NULL, contour = NULL, 
    area = NULL, add.plot = FALSE, colpoints=rep(1, nrow(dfxy)), boxes=TRUE,...)  {

  # Edited s.label so that it accepts other parameters (...), and has options, colpoints, and boxes.
  # colpoints is a vector (or list of colours), the length of which equals the nrow in dfxy
  
    dfxy <- data.frame(dfxy)
    opar <- par(mar = par("mar"))
    on.exit(par(opar))
    par(mar = c(0.1, 0.1, 0.1, 0.1))
    coo <- scatterutil.base(dfxy = dfxy, xax = xax, yax = yax, 
        xlim = xlim, ylim = ylim, grid = grid, addaxes = addaxes, 
        cgrid = cgrid, include.origin = include.origin, origin = origin, 
        sub = sub, csub = csub, possub = possub, pixmap = pixmap, 
        contour = contour, area = area, add.plot = add.plot, ...)
    if (!is.null(neig)) {
        if (is.null(class(neig))) 
            neig <- NULL
        if (class(neig) != "neig") 
            neig <- NULL
        deg <- attr(neig, "degrees")
        if ((length(deg)) != (length(coo$x))) 
            neig <- NULL
    }
    if (!is.null(neig)) {
        fun <- function(x, coo) {
            segments(coo$x[x[1]], coo$y[x[1]], coo$x[x[2]], coo$y[x[2]], 
                lwd = par("lwd") * cneig)
        }
        apply(unclass(neig), 1, fun, coo = coo)
    }
    if (clabel > 0) 
        scatterutil.eti(coo$x, coo$y, label, clabel, boxes=boxes, coul = colpoints, ...)
    if (cpoint > 0) 
        points(coo$x, coo$y, pch = pch, cex = par("cex") * cpoint, col = colpoints,...)
    box()
}