From ligges@statistik.uni-dortmund.de  Sun May 26 09:34:48 2002
From: ligges@statistik.uni-dortmund.de (Uwe Ligges)
Date: Sun, 26 May 2002 10:34:48 +0200
Subject: [R] expressions as axis labels
References: <Pine.A41.4.44.0205251157270.128430-100000@homer17.u.washington.edu>
Message-ID: <3CF09E28.8BB7DDC9@statistik.uni-dortmund.de>

[moved to R-devel]

Thomas Lumley wrote:
> 
> On Sat, 25 May 2002, Patrick Buetzberger wrote:
> 
> > Dear colleagues,
> >
> > I often use chemical formulas to label my x-axis, e.g. in barplots. I
> > used to do this like the following example and it worked just fine:
> >
> <snip>
> >
> > The important point is the x-axis here: before we installed the new R
> > 1.5 on our workstations, the chemical formulas were properly aligned and
> > looked well. Ever since, if I use the exact same procedure, I get the
> > graphic but the chemical formulas are not aligned horizontally properly
> > anymore: e.g. Mg^{2+''} or NO[3]^{-''} are a bit higher than F^{-''} or
> > H^{+''} (it seems to depend on whether there is a subscript or a letter
> > with a part below the main line like a 'g').
> > I didin't find any hint on the r-project homepage. I don't know if we
> > forgot some feature when newly installing R or if something changed in
> > version 1.5.
> 
> I think something changed.  In the NEWS file we have
> 
> o       The vertical alignment of mathematical annotations was wrong.
>         When a vertical adjustment was not given, it was bottom-adjusting
>         i.e,. it was treating adj=0 as adj=c(0, 0).  It now treats
>         adj=0 as adj=c(0, 0.5) as for "normal" text. (PR#1302)
> 
> and I expect this is responsible.  

That change indeed is reasonable, but I don't think it is this
particular change (at least as documented) that makes Patrick's example
doesn't work any more.


> It looks to me as if R is now trying to center the expressions vertically. 

Right for text() and friends, but not for axis(), see the example below,
and maybe this is a bug (Paul?). Anyway, fixing this bug (?) won't
change much for Patrick's example.


> This is also consistent with the previous reply that suggested putting blank 
> subscripts on everything as a work-around.

If sub- or superscripts are a expression, space is added below
respective above that expression (if not already done before), so
complex formulas can be generated. And, at least for me, the result is
somehow expected.

I am very surprised and wondered why Patrick's example worked in
R-1.4.1.
Without having looked into the code, there must have been something
fuzzy that is broken since R-1.5.0.


> I don't think there's a complete fix for this, since sometimes people want
> expressions aligned on their actual vertical centers and sometimes on the
> center of the main line of text (as you do).

Here an example on the alignments:

 plot(1:12, type="n", axes=FALSE)

 expr <- expression(F^{-''}, Cl^{-''}, NO[2]^{-''}, NO[3]^{-''}, 
    PO[4]^{3-''}, SO[4]^{2-''}, Na^{+''}, NH[4]^{+''}, K^{+''},
    Mg^{2+''}, Ca^{2+''}, H^{+''})

 axis(1, 1:12, lab=expr)  # the "problem"

 text(1:12, 3, expr) # adj=c(0.5, 0.5), the default for text()

# This looks like the x-axis annotation:
 text(1:12, 5, expr, adj=c(0.5, 0)) 

# And this is all in *one* formula, as Patrick would like to get it
somehow.
# Only a guess: Was there something like a "coerce to one formula" in
R-1.4.1?

 text(6, 9, 
    labels = expression(F^{-''} * Cl^{-''} * NO[2]^{-''} * NO[3]^{-''} * 
    PO[4]^{3-''} * SO[4]^{2-''} * Na^{+''} * NH[4]^{+''} * K^{+''} *
    Mg^{2+''} * Ca^{2+''} * H^{+''}))


I am sure, Paul will get the point in less than a second.

Uwe Ligges
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[R] expressions as axis labels
Uwe Ligges