make.heatmap: make a heatmap based on matrix values

In coexist: Species coexistence modeling and analysis

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

Author(s)

Youhua Chen <[e-mail]>

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))
            }
        }
    }
  }

Example output

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))
            }
        }
    }
}

coexist documentation built on May 2, 2019, 1:43 p.m.