R/fortify.metaMDS.R

In rasanderson/ggveganextra: Additional functions for vegan and ggvegan

##' @title Fortify a \code{"mataMDS"} object.
##'
##' @description
##' Fortifies an object of class \code{"metaMDS"} to produce a
##' data frame of the selected axis scores in long format, suitable for
##' plotting with \code{\link[ggplot2]{ggplot}}.
##'
##' @details
##' TODO
##'
##' @param  model an object of class \code{"metaMDS"}, the result of a call
##' to \code{\link[vegan]{metaMDS}}.
##' @param data currently ignored.
##' @param ... additional arguments passed to
##' \code{\link[vegan]{scores.metaMDS}}. Note you can't use \code{display}.
##' @return A data frame in long format containing the ordination scores.
##' The first two components are the axis scores.
##' @author Gavin L. Simpson
##'
##' @method fortify metaMDS
##' @export
##'
##' @importFrom ggplot2 fortify
##' @importFrom vegan scores
##'
##' @examples
##' ## load example data
##' require(vegan)
##' data(dune)
##'
##' ord <- metaMDS(dune)
##' head(fortify(ord))
`fortify.metaMDS` <- function(model, data, ...) {
    samp <- scores(model, display = "sites", ...)
    spp <- tryCatch(scores(model, display = "species", ...),
                    error = function(c) {NULL})
    if (!is.null(spp)) {
        df <- rbind(samp, spp)
        df <- as.data.frame(df)
        df <- cbind(Score = factor(rep(c("sites","species"),
                                        c(nrow(samp), nrow(spp)))),
                    Label = c(rownames(samp), rownames(spp)),
                    df)
    } else {
        df <- data.frame(Score = factor(rep("sites", nrow(df))),
                         Label = rownames(samp),
                         samp)
    }
    rownames(df) <- NULL
    df
}