R/showvarparts.R

In vegan: Community Ecology Package

`showvarparts` <-
    function(parts, labels, bg = NULL, alpha=63, Xnames, id.size=1.2, ...)
{
    rad <- 0.725
    ## Default names
    if (missing(Xnames))
        Xnames <- paste("X", seq_len(parts), sep="")
    ## transparent fill colours
    if (!is.null(bg)) {
        bg <- rgb(t(col2rgb(bg)), alpha = alpha, maxColorValue = 255)
        if (length(bg) < parts)
            bg <- rep(bg, length.out = parts)
    }
    ## centroids of circles (parts < 4) or individual fractions (parts
    ## == 4)
    cp <- switch(parts,
                 matrix(c(0,0), ncol=2, byrow=TRUE),
                 matrix(c(0,0, 1,0), ncol=2, byrow=TRUE),
                 matrix(c(0,0, 1,0, 0.5, -sqrt(3/4)), ncol=2, byrow=TRUE),
                 structure(
                     c(-1.2, -0.6, 0.6, 1.2, -0.7, 0, -0.7, 0, 0.7, 0.7,
                       0.3, -0.4, 0.4, -0.3, 0, 0, 0.7, 0.7, 0, 0.3, 0.4,
                       -0.6,-1.2, -0.6, 0.3, -0.7, 0, 0, -0.7, -0.4),
                     .Dim = c(15L, 2L))
                 )
    ## plot limits
    if (parts < 4) {
        xlim <- range(cp[,1]) + c(-rad, rad)
        ylim <- range(cp[,2]) + c(-rad, rad)
    } else {
        xlim <- c(-1.7, 1.7)
        ylim <- c(-1.7, 1.1)
    }
    ## plot
    plot(cp, axes=FALSE, xlab="", ylab="", asp=1, type="n",
         xlim = xlim, ylim = ylim)
    box()
    if (parts < 4) {
        symbols(cp, circles = rep(rad, min(parts,3)), inches = FALSE,
                add=TRUE, bg = bg, ...)
        ## Explanatory data set names added by PL
        if(parts==2) {
            pos.names = matrix(c(-0.65,1.65,0.65,0.65),2,2)
        } else if(parts==3) {
            pos.names = matrix(c(-0.65,1.65,-0.16,0.65,0.65,-1.5),3,2)
        }
        text(pos.names,labels=Xnames[1:parts], cex=id.size)
    } else {
        ## Draw ellipses with veganCovEllipse. Supply 2x2
        ## matrix(c(d,a,a,d), 2, 2) which defines an ellipse of
        ## semi-major axis length sqrt(d+a) semi-minor axis sqrt(d-a).
        d <- 1
        a <- 1/sqrt(2)
        ## Small ellipses X2, X3 at the centroid
        e2 <- veganCovEllipse(matrix(c(d,-a,-a,d), 2, 2))
        e3 <- veganCovEllipse(matrix(c(d, a, a,d), 2, 2))
        ## wider ellipses X1, X4 at sides going through the centroid
        L <- d+a
        W <- (sqrt(L) - sqrt(d-a))^2
        d <- (L+W)/2
        a <- (L-W)/2
        cnt <- sqrt(W/2)
        e1 <- veganCovEllipse(matrix(c(d,-a,-a,d), 2, 2), c(-cnt, -cnt))
        e4 <- veganCovEllipse(matrix(c(d, a, a,d), 2, 2), c( cnt, -cnt))
        polygon(rbind(e1,NA,e2,NA,e3,NA,e4), col = bg, ...)
        ## Explanatory data set names added by PL
        pos.names = matrix(c(-1.62,-1.10,1.10,1.62,0.54,1.00,1.00,0.54),4,2)
        text(pos.names,labels=Xnames[1:4], cex=id.size)
    }

    ## label fractions
    nlabs <- switch(parts, 2, 4, 8, 16)
    if (missing(labels))
        labels <- paste("[", letters[1:nlabs], "]", sep="")
    if (length(labels) != nlabs)
        stop(gettextf("needs %d labels, but input has %d",
                      nlabs, length(labels)))
    switch(parts,
           text(0,0, labels[-nlabs], ...),
           text(rbind(cp, colMeans(cp)), labels[-nlabs], ...),
           text(rbind(cp, colMeans(cp[1:2,]), colMeans(cp[2:3,]),
                      colMeans(cp[c(1,3),]), colMeans(cp)), labels[-nlabs], ...),
           text(cp, labels[-nlabs], ...)
           )
    xy <- par("usr")
    text(xy[2] - 0.05*diff(xy[1:2]), xy[3] + 0.05*diff(xy[3:4]),
         paste("Residuals =", labels[nlabs]), pos = 2, ...)
    invisible()
}