R/points.cca.R

In vegan: Community Ecology Package

`points.cca` <-
    function (x, display = "sites", choices = c(1, 2), scaling = "species",
              arrow.mul, head.arrow = 0.05, select, const, axis.bp = FALSE,
              correlation = FALSE, hill = FALSE, ...)
{
    if (length(display) > 1)
        stop("only one 'display' item can be added in one command")
    pts <- scores(x, choices = choices, display = display, scaling = scaling,
                  const, correlation = correlation, hill = hill, tidy=FALSE,
                  droplist = TRUE)
    if (!missing(select))
        pts <- .checkSelect(select, pts)
    if (display == "cn") {
        cnam <- rownames(pts)
        points(pts, ...)
        pts <- scores(x, choices = choices, display = "bp", scaling = scaling,
                      const, correlation = correlation, hill = hill,
                      droplist = TRUE)
        bnam <- rownames(pts)
        pts <- pts[!(bnam %in% cnam), , drop = FALSE]
        if (nrow(pts) == 0)
            return(invisible())
        else display <- "bp"
    }
    if (display %in% c("bp", "reg", "re", "r")) {
    	if (missing(arrow.mul)) {
            arrow.mul <- ordiArrowMul(pts)
    	}
        pts <- pts * arrow.mul
        arrows(0, 0, pts[, 1], pts[, 2], length = head.arrow,
               ...)
        pts <- pts * 1.1
        if (axis.bp) {
            axis(3, at = c(-arrow.mul, 0, arrow.mul),
                 labels = rep("", 3))
            axis(4, at = c(-arrow.mul, 0, arrow.mul),
                 labels = c(-1, 0, 1))
        }
        return(invisible())
    }
    points(pts, ...)
    invisible()
}