bubbleplot: Bubble Plot

Description

Draw a bubble plot, a scatterplot with varying symbol sizes and colors, or add points to existing plots. A variety of input formats are supported, including vectors, matrices, data frames, formulas, etc.

Usage

bubbleplot(x, ...)
# S3 method for default
bubbleplot(x, y, z, std=TRUE, pow=0.5, add=FALSE,
           rev=FALSE, type="p", ylim=NULL, xlab=NULL, ylab=NULL,
           pch=c(16,1), cex.points=1, col="black", bg=par("bg"), ...)
# S3 method for formula
bubbleplot(formula, data, subset, na.action=NULL, ...)

Arguments

x: a vector of values for the horizontal axis. Can also be a 2-dimensional matrix or table (x values in column names and y values in row names), or a data frame containing x, y, and z in that order. If the data frame contains column names x, y, and z then they will be used for plotting.
...: passed to plot and points.
y: a vector of values for the vertical axis.
z: a vector of values determining the bubble sizes.
std: whether to standardize the z values.
pow: a power coefficient for the bubble sizes.
add: whether to add bubbles to an existing plot.
rev: whether to reverse the y axis.
type: passed to points.
ylim: passed to plot.
xlab, ylab: passed to plot.
pch: passed to points.
cex.points: scales all bubble sizes.
col, bg: passed to points.
formula: has the form z ~ x + y, where z determines the bubble sizes and x and y determine bubble locations.
data: where formula terms are stored, e.g. data frame or list.
subset: a logical vector specifying which data to plot.
na.action: how NA values are handled.

Author

Arni Magnusson.

Details

The std standardization sets z = abs(z) / mean(abs(z)).

The pow = 0.5 (square root) is a good default, where a z value of 2 has twice the area of 1. See example #2 below for an exception, where the z value is tree circumference and therefore proportional to the tree diameter.

The pch, col, and bg arguments can be be vectors of length 2, where positive z values are drawn with pch[1], col[1], bg[1] and negative z values are drawn with pch[2], col[2], and bg[2].

Examples

Run this code

catch.t <- xtabs(Catch~Year+Age, catch.d)              # example table
catch.m <- as.matrix(as.data.frame(unclass(catch.t)))  # example matrix

# 1  Formula
bubbleplot(Catch~Age+Year, data=catch.d)
# Use rev=TRUE to get same layout as crosstab matrix:
print(catch.m)
bubbleplot(Catch~Age+Year, data=catch.d, rev=TRUE, las=1)

# 2  Data frame
bubbleplot(catch.d)
bubbleplot(Orange)
# Visualize tree transverse section at breast height
bubbleplot(Orange, pow=1, cex=2, pch=21,
           col="darkred", bg="peru", lwd=1.5)

# 3  Matrix or table
bubbleplot(catch.m)
bubbleplot(catch.t)

# 4  Positive and negative values
bubbleplot(catch.r)
bubbleplot(Resid~Age+Year, catch.r, subset=Age %in% 4:9,
           rev=TRUE, xlim=c(3.5,9.5), cex=1.3)
# Residuals from orange tree model
library(nlme)
fm <- nlme(circumference~phi1/(1+exp(-(age-phi2)/phi3)),
           fixed=phi1+phi2+phi3~1, random=phi1~1|Tree,
           data=Orange, start=c(phi1=200,phi2=800,phi3=400))
bubbleplot(residuals(fm)~Tree+age, Orange)
bubbleplot(residuals(fm)~Tree+age, Orange, cex=2.5, pch=16,
           col=c("dodgerblue","orange"))

# 5  Richter magnitude, amplitude, and energy release
bubbleplot(mag~long+lat, quakes, pch=1)
bubbleplot(10^mag~long+lat, quakes, cex=1.2, col=gray(0, 0.3))
bubbleplot(sqrt(1000)^mag~long+lat, quakes, cex=1.2, col=gray(0, 0.3))
bubbleplot(sqrt(1000)^mag~long+lat, quakes, cex=1.2, col="#FF00004D")