There is a function, gap.barplot for doing that in the plotrix package, but I was not happy with the way the result looked, so I made it my own way using subplot in the TeachingDemos library.
data=data.frame(R=c(120,11),U=c(32,1),C=c(12,3),G=c(4,0)
,J=c(6,0),I=c(3,2),N=c(4,0))
# I want to plot the lower values up to 55, then a split to 95 for the
# last top. This should make it clear which is the highest, without
# drowning out the other data.
# Setting up an outer wireframe for the plots. I want the split to be
# approx 5% of the scale,
# I am to plot the ranges 0 - 55 and 95 - 140, in total 10 decades, I
# multiply that with 2 and add 5 and get 21 units on the outer
# Y axis:
plot(c(0,1),c(0,21),type='n',axes=FALSE,ylab="Number of something",xlab='')
# Plotting the lower range in the lower 11/21 of the plot.
# xpd=FALSE to clip the bars
subplot(barplot(as.matrix(data),col=heat.colors(2),ylim=c(0,55)
,xpd=FALSE,las=3),x=c(0,1),y=c(0,11))
# Plotting the upper range in the upper 9/21 of the plot, 1/21 left to
# the split. Again xpd=FALSE, names.arg is set up to avoid having
# the names plotted here, must be some easier way to do this but
# this works
subplot(barplot(as.matrix(data),col=heat.colors(2),ylim=c(95,140),xpd=FALSE,
names.arg=c('','','','','','','')), x=c(0,1),y=c(12,21))
# Legend. An annoiance is that the colors comes in the opposite
# order than in the plot.
legend("topright",c('Group 1','Group 2'),fill=heat.colors(2))
# so far so good. (Just run the upper part to see the result so far
# Just want to make the ends of the axes a bit nicer.
# All the following plots are in units of the outer coordinate system
lowertop=11.1 # Where to end the lower axis
breakheight=0.5 # Height of the break
upperbot=lowertop+breakheight # Where to start the upper axes
markerheight=0.4 # Heightdifference for the break markers
markerwidth=.04 # With of the break markers
# Draw the break markers:
lines(c(0,0),c(1,lowertop))
lines(c(markerwidth/-2,markerwidth/2),
c(lowertop-markerheight/2,lowertop+markerheight/2))
lines(c(0,0),c(upperbot,14))
lines(c(markerwidth/-2,markerwidth/2),
c(upperbot-markerheight/2,upperbot+markerheight/2))
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TODO: rewrite to use par(fig) to be able to do without any external libraries.