Multi panel figure with inset plots in base graphics

gistfile1.r

## OK, this turned out to be more complicated than I would have
## thought.  I feel that this approach *should* work, but it confuses
## R's multi-panel plots:

## Smaller margins, plus a top margin
par(mar=c(3.1, 3.1, .5, .5), oma=c(0, 0, 1.5, 0), mfrow=c(2, 2))

## Plot dummy data
plot(1:10)

## New coordinates relative to the plot (20% of the height and width,
## inset by 10 % at the bottom and 5% on the right), within the
## boundaries of the plot box.
p <- c(.75, .95, .10, .25)

fig.new <- c(grconvertX(p[1:2], from="npc", to="ndc"),
             grconvertY(p[3:4], from="npc", to="ndc"))

op <- par(fig=fig.new, cex=.5, new=TRUE, mar=rep(0, 4))
## Plot the inset
plot(1:10, col="red")
## Reset the parameters
par(op)

## Gah - this replaces the current plot
plot(1:10)
## Worse - this won't advance things.

dev.off()

## I tried using layout instead of mfrow, but that didn't help either.

## Instead, you'll have to get the inset coordinates on the first pass
## and add the insets after:

## Smaller margins, plus a top margin
par(mar=c(3.1, 3.1, .5, .5), oma=c(0, 0, 1.5, 0), mfrow=c(2, 2))

## Plot dummy data
plot(1:10)
fig.new.1 <- c(grconvertX(p[1:2], from="npc", to="ndc"),
               grconvertY(p[3:4], from="npc", to="ndc"))
plot(1:10)
fig.new.2 <- c(grconvertX(p[1:2], from="npc", to="ndc"),
               grconvertY(p[3:4], from="npc", to="ndc"))
plot(1:10)
fig.new.3 <- c(grconvertX(p[1:2], from="npc", to="ndc"),
               grconvertY(p[3:4], from="npc", to="ndc"))
plot(1:10)
fig.new.4 <- c(grconvertX(p[1:2], from="npc", to="ndc"),
               grconvertY(p[3:4], from="npc", to="ndc"))

op <- par(fig=fig.new.1, cex=.5, new=TRUE, mar=rep(0, 4))
plot(1:10, col="red")
par(op)

op <- par(fig=fig.new.2, cex=.5, new=TRUE, mar=rep(0, 4))
plot(1:10, col="purple")
par(op)

op <- par(fig=fig.new.3, cex=.5, new=TRUE, mar=rep(0, 4))
plot(1:10, col="green")
par(op)

op <- par(fig=fig.new.4, cex=.5, new=TRUE, mar=rep(0, 4))
plot(1:10, col="blue")
par(op)