[R] barplot2, gap.barplot

[Marc Schwartz]

On Fri, 2007-03-02 at 10:07 -0600, hadley wickham wrote:
> On 3/2/07, Marc Schwartz <marc_schwartz at comcast.net> wrote:
> > On Fri, 2007-03-02 at 08:53 -0600, hadley wickham wrote:
> > > > 3. Depending on the nature of your data, if the extreme value is
> > > > representative of an important marked difference relative to the other
> > > > values, then I don't particularly find the 'look' of the plot to be
> > > > overly problematic. It does appropriately emphasize the large
> > > > difference.
> > > >
> > > > On the other hand, you might want to consider using a log scale on the y
> > > > axis as an alternative to an axis gap. This would be a reasonable
> > > > approach to plotting values that have a notable difference in range.  If
> > > > you do this, note that you would need to ensure that all y values are >0
> > > > (ie. y axis range minimum, lower bounds of CI's, etc.) since:
> > > >
> > > > > log10(0)
> > > > [1] -Inf
> > > >
> > > >
> > >
> > > Of course, you can't do this with a bar plot, because bars should be
> > > anchored at 0.
> >
> > Both barplot() and barplot2() support log scaling for both x and y axes.
> >
> > In both functions, the default axis minimum for the 'height' axis (y by
> > default, x if 'horizontal = TRUE') will be 0.9 * min(height) to avert
> > log10(0) related issues. Errors will be issued otherwise if any values
> > of 'height' are <= 0 or 'ylim'/'xlim' args are similarly set.
> 
> I think that's a pretty bad idea - in a bar plot you are comparing the
> ratio of heights of the bars, not the absolute heights.  It's the same
> reason it's a bad idea to have a bar graph with a non-0 y-axis - it's
> misleading.

Hadley,

I might note that even lattice will do this, arguably easier than
barplot[2]():

library(lattice)
x <- 10 ^ (0:10)
barchart(x ~ 0:10, horizontal = FALSE, 
         scales = list(y = list(log = 10)))


Is it the right thing to do?  I'll leave that for others to debate. I
have stronger feelings on the 'gapped axis' issue.

I don't tend to use bar plots too much myself any longer and it all
depends upon the audience.

There have been requests for log scales on barplots on the R lists going
back several years, which is one of the reasons that I wrote barplot2()
some years ago.  It was also one of my first exercises in gaining a
lower level understanding of R's graphics models.

The 'log' and 'add' arguments and related code from barplot2() were then
included in R's barplot() in version 2.2.0, I believe by Paul.

HTH,

Marc