image2 {popbio}R Documentation

Display a matrix image

Description

Creates a grid of colored rectangles to display a projection, elasticity, sensitivity or other matrix.

Usage

image2(x, col = c("white", rev(heat.colors(23))), breaks, log = TRUE,
 border = NA, box.offset = 0, round = 3, cex, text.cex = 1, 
 text.col = "black", mar = c(1, 3, 3, 1), 
 labels = 2:3, label.offset = 0.2, label.cex = 1)

Arguments

x A numeric matrix with row and column names
col A vector of colors for boxes
breaks A numeric vector of break points or number of intervals into which x is to be cut. Default is the length of col
log Cut values in x using a log scale, default TRUE
border The border color for boxes, default is no borders
box.offset Percent reduction in box size (a number between 0 and 1), default is no reduction
round Number of decimal places to display values of x in each box
cex Magnification size of text and labels, if specified this will replace values in both text.cex and label.cex
text.cex Magnification size of text in cells only
text.col Color of text in cells, use NA to skip text labels
mar Margins on four sides of plot
labels A vector giving sides of the plot (1=bottom, 2=left, 3=top, 4=right) for row and column labels
label.offset Amount of space between label and boxes
label.cex Magnification size of labels

Details

The minimum value in x is usually assigned to the first color category and the rest of the values are then cut into equally spaced intervals. This was added to show transitions with very low probabilities in a new color category, eg, 2e-06 would ususally be grouped with 0 using image. Note if all elements > 0, then the first color will not be used.

Value

A image plot of the matrix in x

Author(s)

Chris Stubben

See Also

image

Examples

data(calathea)

op<-par(mfrow=c(2,2))
image2(calathea[[11]], text.cex=.8)
## labels on bottom right
image2( calathea[[11]], text.cex=.8, labels=c(1,4), mar=c(3,1,1,3))
## no text
image2( calathea[[11]], text.col=NA)
## with smaller boxes and gray border
image2( calathea[[11]], text.cex=.8, box.offset=0.2, border="gray70")

## if comparing two or more matrices, get the log10 range
## of values (not including zero) and pass to breaks
x<-unlist(calathea)
x<-log10(range(x[x!=0]))
par(mfrow=c(4,4))
for(i in 1:16)
  {
image2( calathea[[i]], cex=.7, breaks=seq(x[1], x[2], len=24))
  title(names(calathea[i]), line=3)
}
par(op)

## sometimes log scale is not needed
data(tortoise)
A<-tortoise$T + tortoise$F.med.high
image2(A, log=FALSE, box.offset=0.1)

[Package popbio version 1.1.11 Index]