R/plot.nestedtemp.R

In vegan: Community Ecology Package

### plot() methods for those nested* functions that return sufficient
### data to draw a plot. We display a plot using image() with coloured
### rectangles for occurrences or colours dependent on the
### contribution to the nestedness when appropriate.

`plot.nestedtemp` <-
    function (x, kind = c("temperature", "incidence"),
              col = rev(heat.colors(100)), names = FALSE,  
              ...) 
{
    kind <- match.arg(kind)
    if (kind == "temperature") 
        z <- x$u
    else z <- x$comm
    z <- t(z[nrow(z):1, ])
    image(z, axes = FALSE, col = col, ...)
    box()
    lines(x$smooth$x, 1 - x$smooth$y)
    if (length(names) == 1)
        names <- rep(names, 2)
    if (names[1]) {
        axis(2, at = seq(1, 0, len = nrow(x$u)), labels = rownames(x$u),
            las = 2, ...)
    }
    if (names[2]) {
        axis(3, at = seq(0, 1, len = ncol(x$u)), labels = colnames(x$u),
            las = 2, ...)
    }
}

`plot.nestednodf` <-
    function(x, col = "red", names = FALSE, ...)
{
    z <- x$comm
    z <- t(z[nrow(z):1,])
    if (length(col) == 1)
        col <- c(NA, col)
    image(z, axes = FALSE, col = col, ...)
    box()
    if (length(names) == 1)
        names <- rep(names, 2)
    if (names[1]) {
        axis(2, at = seq(1, 0, len = ncol(z)), labels = rev(colnames(z)),
            las = 2, ...)
    }
    if (names[2]) {
        axis(3, at = seq(0, 1, len = nrow(z)), labels = rownames(z),
            las = 2, ...)
    }
}