plotrix (version 2.6-1)

color2D.matplot: Display a numeric matrix as color matrix

Description

Display the values of a numeric 2D matrix or data frame as colored rectangles or hexagons.

Usage

color2D.matplot(x,redrange=c(0,1),greenrange=c(0,1),bluerange=c(0,1),
  extremes=NA,cellcolors=NA,show.legend=FALSE,nslices=10,xlab="Column",
  ylab="Row",do.hex=FALSE,axes=TRUE,show.values=FALSE,vcol="white",vcex=1,
  border="black",na.color=NA,...)

Arguments

x

data values

redrange, greenrange, bluerange

the ranges of red, green and blue that will be scaled to represent the range of numeric values

extremes

The colors for the extreme values of x. Takes precedence over the color ranges.

cellcolors

A precalculated vector of cell colors. This must have exactly the same number of colors as there are values in the matrix or it will be uninformative. Takes precedence over both extremes and color ranges.

show.legend

whether to display a color legend with the extreme numeric values in the lower left corner of the plot. If the default is not suitable, call color.legend separately.

nslices

The number of color "slices" in the legend.

xlab,ylab

axis labels for the plot.

do.hex

plot packed hexagons instead of rectangles.

axes

Whether to suppress the default axis labelling.

show.values

Whether to display the numeric values of x. This also controls the number of decimal places displayed.

vcol

The color for the value display.

vcex

The character expansion for the value display.

border

The color(s) for the borders of the cells. Pass NA if no border is wanted.

na.color

The color to use for NA values of x.

...

arguments passed to plot.

Value

• nil

Details

Displays a plot with the same number of rectangular or hexagonal cells as there are numeric values in the matrix or data frame. Each rectangle is colored to represent its corresponding value. The rectangles are arranged in the conventional display of a 2D matrix with rows beginning at the top and columns at the left. The color scale defaults to black for the minimum value and white for the maximum. The user will have to adjust the plot device dimensions to get regular squares or hexagons, especially when the matrix is not square. As the margins are not equivalent for all display devices, this is currently a matter of trial and error. Drawing hexagons is quite slow. show.values is also used to control the number of decimal places displayed if the values are shown. TRUE will give one decimal place, 2 two, and so on.

See Also

color.scale, image

Examples

x<-matrix(rnorm(1024)+sin(seq(0,2*pi,length=1024)),nrow=32)
 color2D.matplot(x,c(1,0),c(0,0),c(0,1),show.legend=TRUE,
  xlab="Columns",ylab="Rows",main="2D matrix plot")
 # generate colors that show negative values in red and positive in green
 cellcol<-matrix(rep("#000000",1024),nrow=32)
 cellcol[x<0]<-color.scale(x[x<0],c(1,0.8),c(0,0.8),0)
 cellcol[x>0]<-color.scale(x[x>0],0,c(0.8,1),c(0.8,0))
 # now do hexagons without borders
 color2D.matplot(x,cellcolors=cellcol,xlab="Columns",ylab="Rows",
  do.hex=TRUE,main="2D matrix plot (hexagons)",border=NA)
 # for this one, we have to do the color legend separately
 # because of the two part color scaling
 legval<-seq(min(x),max(x),length.out=6)
 legcol<-rep("#000000",6)
 legcol[legval<0]<-color.scale(legval[legval<0],c(1,0.8),c(0,0.8),0)
 legcol[legval>0]<-color.scale(legval[legval>0],0,c(0.8,1),c(0.8,0))
 color.legend(0,-5,6,-4,round(c(min(x),0,max(x)),1),rect.col=legcol)
 # do a color only association plot
 xt<-table(sample(1:10,100,TRUE),sample(1:10,100,TRUE))
 observed<-xt[,rev(1:dim(xt)[2])]
 expected<-outer(rowSums(observed),colSums(observed),"*")/sum(xt)
 deviates<-(observed-expected)/sqrt(expected)
 cellcol<-matrix(rep("#000000",100),nrow=10)
 cellcol[deviates<0]<-
  color.scale(deviates[deviates<0],c(1,0.8),c(0,0.5),0)
 cellcol[deviates>0]<-
  color.scale(deviates[deviates>0],0,c(0.7,0.8),c(0.5,0))
 color2D.matplot(x=round(deviates,2),cellcolors=cellcol,
  show.values=TRUE,main="Association plot")