# Area Plots with Intensity Coloring

July 13, 2010
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I am not sure apeescape’s ggplot2 area plot with intensity colouring is really the best way of presenting the information, but it had me intrigued enough to replicate it using base R graphics.

The key technique is to draw a gradient line which R does not support natively so we have to roll our own code for that. Unfortunately, `lines(..., type="l")` does not recycle the colour `col=` argument, so we end up with rather more loops than I thought would be necessary.

(The answer is not to use `lines(..., type="h")` which, confusingly, does recycle the colour `col=` argument. This one had me for a while, but the `type=h` lines always start from zero so you do not get the gradient feature.)

We also get a nice opportunity to use the under-appreciated `read.fwf` function.

```##!/usr/bin/Rscript
## nino.R - another version of http://bit.ly/9P9Gh1

## Get the data from the NOAA server
widths=c(-1, 9, rep(c(-5, 4, 4), 4)),
skip=4,
col.names=c("Week",
paste(rep(c("Nino12","Nino3","Nino34","Nino4"), rep(2, 4)),
c("SST", "SSTA"), sep=".")))

## Make the date column something useful
nino\$Week <- as.Date(nino\$Week, format="%d%b%Y")

ncol <- 50

## Make plot
plot(Nino34.SSTA ~ Week, data=nino, type="n",
main="Nino34", xlab="Date", ylab="SSTA", axes=FALSE)
do.call(function (...) rect(..., col="gray85", border=NA),
as.list(par("usr")[c(1, 3, 2, 4)]))

y <- nino\$Nino34.SSTA                   # The values we will plot
x <- nino\$Week

axis.Date(1, x=x, tck=1, col="white")
axis(2, tck=1, col="white")
box()

idx <- integer(NROW(nino))
idx[y >= 0] <- 1 + round( y[y >= 0] * (ncol - 1) / max( y[y >= 0]), 0)
idx[y <  0] <- 1 + round(-y[y <  0] * (ncol - 1) / max(-y[y <  0]), 0)

draw.gradient <- function(x, ys, cols) {
xs <- rep(x, 2)
for (i in seq(1, length(ys)-1))
plot.xy(list(x=xs, y=c(ys[i], ys[i+1])), type="l", col=cols[i])
}

for (i in 1:length(x)) {
ys <- seq(0, y[i], length.out=idx[i]+1)
}
```

The result is a decent gradient:

I deliberately omitted the scale legend on the right hand side following Allan’s First Law of Happy Graphics: Thou shall not present the same information twice.

For less dense information, you should increase the line width. That is left to the reader. (Hint: it is hard to get just right in base graphics, but `lwd <- ceiling(par("pin")[1] / dev.size("in")[1] * dev.size("px")[1] / length(x))` could be a starting point for an approximation. We really need gradient-filled polygons in base R.)

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