coexist (version 1.0)

make.heatmap: make a heatmap based on matrix values

Description

make a heatmap based on matrix values

Usage

make.heatmap(mat, type = "gray", xname = "x", yname = "y", xlab = NULL, ylab = NULL, title = NULL)

Arguments

mat

the coexistence density matrix under the two parameter value combination (x and y)

type

currently only support the "gray" density heatmap

xname

name for parameter x at the horizontal axis

yname

name for parameter y at the vertical axis

xlab

parameter x's sampling point vector, for example, c(.1,.3,.6,.9), something like that..

ylab

parameter y's sampling point vector, for example, c(.1,.3,.6,.9), something like that..

title

main text for the figure

References

Chen YH (2012) coexist: an R package for performing species coexistence modeling and analysis under asymmetric dispersal and fluctuating source-sink dynamics. http://code.google.com/p/coexist.

See Also

batch.pdf.pairpar, batch.pdf.onepar

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (mat, type = "gray", xname = "x", yname = "y", xlab = NULL, 
    ylab = NULL, title = NULL) 
{
    xrange <- dim(mat)[2] + 1
    yrange <- dim(mat)[1] + 1
    if (xrange >= yrange) {
        maxrange <- xrange
        xscale = 1
        yscale <- yrange/xrange
    }
    if (yrange > xrange) {
        maxrange <- yrange
        xscale <- xrange/yrange
        yscale = 1
    }
    maxnum = ceiling(max(as.vector(mat)))
    tmat <- t(mat)
    plot((1:maxrange) * xscale, (1:maxrange) * yscale, type = "n", 
        xlab = xname, ylab = yname, axes = F)
    if (length(xlab) != 0) {
        axis(1, at = c(1:(xrange - 1)) + 0.5, labels = xlab)
    }
    else {
        axis(1, at = c(1:(xrange - 1)) + 0.5, labels = c(1:(xrange - 
            1)))
    }
    if (length(ylab) != 0) {
        axis(2, at = c(1:(yrange - 1)) + 0.5, labels = ylab)
    }
    else {
        axis(2, at = c(1:(yrange - 1)) + 0.5, labels = c(1:(yrange - 
            1)))
    }
    if (length(title) != 0) {
        mtext(title)
    }
    for (i in 1:(xrange - 1)) {
        for (j in 1:(yrange - 1)) {
            value = tmat[i, j]
            x1 = i
            x2 = i + 1
            y1 = j
            y2 = j + 1
            if (type == "gray") {
                rect(x1, y1, x2, y2, col = gray((maxnum - value)/maxnum), 
                  border = gray((maxnum - value)/maxnum))
            }
        }
    }
  }