R/autoplot.isomap.R

In gavinsimpson/ggvegan: 'ggplot2' Plots for the 'vegan' Package

#' @title ggplot-based plot for objects of class \code{"isomap"}
#'
#' @description
#' Produces a multi-layer ggplot object representing the output of objects produced by \code{\link[vegan]{isomap}}.
#'
#' @param object an object of class \code{"isomap"}, the result of a call to \code{\link[vegan]{isomap}}.
#' @param axes numeric; which axes to plot, given as a vector of length 2.
#' @param geom character; which geom to use for the MDS scores layer.
#' @param network logical; should the edges of the ISOMAP network be drawn?
#' @param line.col colour with which to draw the network edges.
#' @param size numeric; size aesthetic for the log-series curve.
#' @param xlab character; label for the x-axis.
#' @param ylab character; label for the y-axis.
#' @param title character; subtitle for the plot.
#' @param subtitle character; subtitle for the plot.
#' @param caption character; caption for the plot.
#' @param ... additional arguments passed to other methods.
#' @return A ggplot object.
#' @author Gavin L. Simpson
#'
#' @export
#'
#' @importFrom ggplot2 ggplot autoplot geom_point geom_segment aes_string labs fortify coord_fixed
#'
#' @examples
#'
#' data(BCI)
#' dis <- vegdist(BCI)
#' ord <- isomap(dis, k = 3)
#'
#' autoplot(ord)
#'
#' autoplot(ord, geom = "text")
`autoplot.isomap` <- function(object, axes = c(1,2),
                              geom = c("point", "text"),
                              network = TRUE,
                              line.col = "grey85", size = 0.7,
                              xlab = NULL, ylab = NULL,
                              title = "Isometric feature mapping",
                              subtitle = NULL, caption = NULL,
                              ...) {
    pts <- fortify(object, axes = axes)
    net <- fortify(object, axes = axes, what = "network")

    vars <- paste0("Dim", axes)
    plt <- ggplot(pts, aes_string(x = vars[1], y = vars[2]))

    if (isTRUE(network)) {
        plt <- plt +
            geom_segment(data = net,
                         mapping = aes_string(x = "xfrom",
                                              y = "yfrom",
                                              xend = "xto",
                                              yend = "yto"),
                         colour = line.col, size = size)
    }

    ## match the geom
    geom <- match.arg(geom)
    point <- TRUE
    if (isTRUE(all.equal(geom, "text"))) {
        point <- FALSE
    }

    plt <- if (point) {
               plt + geom_point()
           } else {
               plt + geom_text(aes_string(label = "label"))
           }

    if (is.null(xlab)) {
        xlab = vars[1]
    }
    if (is.null(ylab)) {
        ylab = vars[2]
    }

    plt <- plt + labs(x = xlab, y = ylab, title = title, subtitle = subtitle,
                      caption = caption) +
        coord_fixed()

    plt
}