plotBubbles: Construct a Bubble Plot from a Matrix

Description

Construct a bubble plot for a matrix z.

Usage

plotBubbles(z, xval=FALSE, yval=FALSE, dnam=FALSE, rpro=FALSE, 
   cpro=FALSE, rres=FALSE, cres=FALSE, powr=0.5, size=0.2, lwd=1,
   clrs=c("black","red","blue"), hide0=FALSE, frange=0.1, prettyaxis=FALSE, ...)

Arguments

z: input matrix, array (2 dimensions) or data frame.
xval: x-values and/or labels for the columns of z. if xval=TRUE, the first row contains x-values for the columns.
yval: y-values and/or labels for the rows of z. If yval=TRUE, the first column contains y-values for the rows.
dnam: logical: if TRUE, attempt to use dimnames of input matrix z as xval and yval. The dimnames are converted to numeric values and must be strictly increasing or decreasing. If successful, these values will overwrite previously specified values of xval and yval or any default indices.
rpro: logical: if TRUE, convert rows to proportions.
cpro: logical: if TRUE, convert columns to proportions.
rres: logical: if TRUE, use row residuals (subtract row means).
cres: logical: if TRUE, use column residuals (subtract column means).
powr: power transform. Radii are proportional to z^powr. Note: powr=0.5 yields bubble areas proportional to z.
size: size (inches) of the largest bubble.
lwd: line width for drawing circles.
clrs: colours (3-element vector) used for positive, negative, and zero values, respectively.
hide0: logical: if TRUE, hide zero-value bubbles.
frange: number specifying the fraction by which the range of the axes should be extended.
prettyaxis: logical: if TRUE, apply the pretty function to both axes.
...: additional arguments for plotting functions.

Author

Jon T. Schnute, Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo BC

Details

The function plotBubbles essentially flips the z matrix visually. The columns of z become the x-values while the rows of z become the y-values, where the first row is displayed as the bottom y-value and the last row is displayed as the top y-value. The function's original intention was to display proportions-at-age vs. year.

Examples

Run this code

local(envir=.PBSmodEnv,expr={
  oldpar = par(no.readonly=TRUE)
  plotBubbles(round(genMatrix(40,20),0),clrs=c("green","grey","red"));
  data(CCA.qbr,envir=.PBSmodEnv)
  plotBubbles(CCA.qbr,cpro=TRUE,powr=.5,dnam=TRUE,size=.15,
    ylim=c(0,70),xlab="Year",ylab="Quillback Rockfish Age")
  par(oldpar)
})