Permalink
Find file Copy path
Fetching contributors…
Cannot retrieve contributors at this time
131 lines (129 sloc) 5.32 KB
##' @title ggplot-based plot for objects of class \code{"cca"}
##'
##' @description
##' Produces a multi-layer ggplot object representing the output of objects produced by \code{\link[vegan]{cca}}, or \code{\link[vegan]{capscale}}.
##'
##' @details
##' TODO
##'
##' @param object an object of class \code{"cca"}, the result of a call to \code{\link[vegan]{cca}} or \code{\link[vegan]{capscale}}.
##' @param axes numeric; which axes to plot, given as a vector of length 2.
##' @param geom character; which geoms to use for the layers. Can be a
##' vector of length equal to \code{length(display)}, in which case the
##' \emph{i}th element of \code{type} refers to the \emph{i}th element
##' of \code{display}.
##' @param layers character; which scores to plot as layers
##' @param legend.position character or two-element numeric vector; where to position the legend. See \code{\link[ggplot2]{theme}} for details. Use \code{"none"} to not draw the legend.
##' @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 const General scaling constant to \code{rda} scores. See
##' \code{\link[vegan]{plot.cca}} for details.
##' @param ... Additional arguments passed to \code{\link{fortify.cca}}.
##' @return Returns a ggplot object.
##' @author Gavin L. Simpson
##'
##' @export
##'
##' @importFrom grid arrow unit
##' @importFrom ggplot2 autoplot ggplot geom_point geom_text geom_segment labs coord_fixed aes_string
##'
##' @examples
##' data(dune)
##' data(dune.env)
##'
##' sol <- cca(dune ~ A1 + Management, data = dune.env)
##' autoplot(sol)
`autoplot.cca` <- function(object, axes = c(1,2), geom = c("point", "text"),
layers = c("species", "sites", "biplot", "centroids"),
legend.position = "right",
title = NULL, subtitle = NULL, caption = NULL,
ylab, xlab, const, ...) {
axes <- rep(axes, length.out = 2L)
obj <- fortify(object, axes = axes, ...)
LAYERS <- levels(obj$Score)
## sort out x, y aesthetics
vars <- getDimensionNames(obj)
## match the geom
geom <- match.arg(geom)
point <- TRUE
if (isTRUE(all.equal(geom, "text"))) {
point <- FALSE
}
## subset out the layers wanted
### need something here first to match acceptable ones?
### or just check that the layers selected would return a df with
### at least 1 row.
obj <- obj[obj$Score %in% layers, , drop = FALSE]
## skeleton layer
plt <- ggplot()
## add plot layers as required
want <- obj$Score %in% c("species", "sites")
if (point) {
plt <- plt +
geom_point(data = obj[want, , drop = FALSE ],
aes_string(x = vars[1], y = vars[2], shape = 'Score',
colour = 'Score'))
} else {
plt <- plt +
geom_text(data = obj[want, , drop = FALSE ],
aes_string(x = vars[1], y = vars[2], label = 'Label',
colour = 'Score'))
}
## remove biplot arrows for centroids if present
if(all(c("biplot","centroids") %in% LAYERS)) {
want <- obj$Score == "biplot"
tmp <- obj[want, ]
obj <- obj[!want, ]
bnam <- tmp[, "Label"]
cnam <- obj[obj$Score == "centroids", "Label"]
obj <- rbind(obj, tmp[!bnam %in% cnam, , drop = FALSE])
}
if(any(want <- obj$Score == "constraints")) {
if (point) {
plt <- plt + geom_point(data = obj[want, , drop = FALSE ],
aes_string(x = vars[1], y = vars[2]))
} else {
plt <- plt + geom_text(data = obj[want, , drop = FALSE ],
aes_string(x = vars[1], y = vars[2],
label = 'Label'))
}
}
if(any(want <- obj$Score == "biplot")) {
if (length(layers) > 1) {
mul <- arrowMul(obj[want, vars, drop = FALSE],
obj[!want, vars, drop = FALSE])
obj[want, vars] <- mul * obj[want, vars]
}
col <- "navy"
plt <- plt +
geom_segment(data = obj[want, , drop = FALSE ],
aes_string(x = 0, y = 0, xend = vars[1], yend = vars[2]),
arrow = arrow(length = unit(0.2, "cm")),
colour = col)
obj[want, vars] <- 1.1 * obj[want, vars]
plt <- plt + geom_text(data = obj[want, , drop = FALSE ],
aes_string(x = vars[1], y = vars[2], label = 'Label'))
}
if(any(want <- obj$Score == "centroids")) {
plt <- plt + geom_text(data = obj[want, , drop = FALSE ],
aes_string(x = vars[1], y = vars[2], label = 'Label'),
colour = "navy")
}
if(missing(xlab)) {
xlab <- vars[1]
}
if(missing(ylab)) {
ylab <- vars[2]
}
plt <- plt + labs(x = xlab, y = ylab, title = title, subtitle = subtitle,
caption = caption)
## add equal scaling
plt <- plt + coord_fixed(ratio = 1)
## do we want a legend
plt <- plt + theme(legend.position = legend.position)
plt
}
## `aplot.cca` <- `autoplot.cca`