R/ord_labels.R

In jfq3/ggordiplots: Make 'ggplot2' Versions of Vegan's Ordiplots

#' Make Ordination Axis Labels
#'
#' Makes ordination axis labels that include, if appropriate, the \% total variance explained by each axis.
#'
#' @param ord A vegan ordination object.
#'
#' @return A character vector, each element of which can be used to label the corresponding axis of an ordination plot.
#'
#' @details If there are no eigenvalues in ord, or if any eigenvalues are less than 0, each element of the vector returned has the form "DIMn" where n is the axis number. Otherwise, each element of the vector returned has the form "AxisN xx.x\%" where "Axis" is taken from the vector of eigenvalues in ord if they are named or simply "DIM" if they are not, N is the number of the axis, and xx.x is the \% of total variance explained by the axis.
#'
#' @export
#' @examples
#' data("dune")
#' data("dune.env")
#' dune_hel <- decostand(dune, method = "hellinger")
#' ord <- rda(dune_hel)
#' axis_labels <- ord_labels(ord)
#' axis_labels[c(1,2)]
#'
ord_labels <-
  function(ord){
    ev <- vegan::eigenvals(ord)
    if (!is.na(ev)[1]) {
      tol <- -(1e-07)*ev[1]
      ord.labels <- rep("", length(ev))
      if ((any(is.na(ev))) | (any(ev < tol))) {
        for ( i in 1:length(ev)) {
          ord.labels[i] <- paste("DIM", i, sep = "")
        }
      }
      else {
        ev.pc <- round(100*(ev/sum(ev)), 2)
        axis.names <- names(ev)
        if (is.null(axis.names)) {
          for ( i in 1:length(ev.pc)) {
            ord.labels[i] <- paste("DIM", i, " ", sprintf(ev.pc[i], fmt = '%#.1f'), "%", sep="")
          }
        } else {
          for (i in 1:length(ev.pc)){
            ord.labels[i] <- paste(axis.names[i], " ", ev.pc[i],"%", sep="")
          }
        }
      }
    } else {
      ord.labels <- colnames(vegan::scores(ord, display = "sites"))
    }

    return(ord.labels)
  }