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bug in plot.table(..., log='y')?

6 messages · Spencer Graves, Duncan Murdoch, Martin Maechler +1 more

Original
Spencer Graves
# 
Dear R Developers:


	  Consider the following example:


(tstTable <- table(rep(1:3, 3:1)))
plot(tstTable)
plot(tstTable, log='y')


	  "plot(tstTable)" works as expected.  "plot(tstTable, log='y')" gives 
a warning:


Warning message:
In plot.window(...) :
   nonfinite axis=2 limits [GScale(-inf,0.477121,..); log=TRUE] -- 
corrected now


	  AND the plot has a y axis scale running from 1e-307 to 1e+13.


	  This is with R 4.2.0 (R Console and the current RStudio) under macOS 
11.6.6.


	  "plot(as.numeric(names(tstTable), as.numeric(tstTable), log='y'))" 
works as expected ;-)


	  Comments?
	  Thanks for your valuable work in making it easier for people 
everywhere to do quality statistics.


	  Spencer Graves
R version 4.2.0 (2022-04-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.6.6

Matrix products: default
LAPACK: 
/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods
[7] base

loaded via a namespace (and not attached):
[1] compiler_4.2.0 tools_4.2.0    knitr_1.39     xfun_0.30
Duncan Murdoch
#
On 28/05/2022 11:33 a.m., Spencer Graves wrote:
The help page ?plot.table says that ylim defaults to c(0, max(x)), i.e. 
c(0,3) in your example.  If you're asking to plot that on a log scale, 
there are bound to be problems.

If you specify ylim, e.g. as c(min(tstTable), max(tstTable)), things are 
fine in your example; they won't be in examples where the min is zero.

Duncan Murdoch
Spencer Graves
#
On 5/28/22 11:23 AM, Duncan Murdoch wrote:
Thanks.  I looked at the help file but didn't read it carefully enough.


	  Spencer
1 day later
Martin Maechler
# 

        
> On 5/28/22 11:23 AM, Duncan Murdoch wrote:

        
>> On 28/05/2022 11:33 a.m., Spencer Graves wrote:

        
>>> Dear R Developers:
    >>> 
    >>> 
    >>> ????? Consider the following example:
    >>> 
    >>> 
    >>> (tstTable <- table(rep(1:3, 3:1))) plot(tstTable)
    >>> plot(tstTable, log='y')
    >>> 
    >>> 
    >>> ????? "plot(tstTable)" works as expected.?
    >>> "plot(tstTable, log='y')" gives a warning:
    >>> 
    >>> 
    >>> Warning message: In plot.window(...) : ??? nonfinite
    >>> axis=2 limits [GScale(-inf,0.477121,..); log=TRUE] --
    >>> corrected now
    >>> 
    >>> 
    >>> ????? AND the plot has a y axis scale running from
    >>> 1e-307 to 1e+13.
    >>> 
    >>> 
    >>> ????? This is with R 4.2.0 (R Console and the current
    >>> RStudio) under macOS 11.6.6.
    >>> 
    >>> 
    >>> ????? "plot(as.numeric(names(tstTable),
    >>> as.numeric(tstTable), log='y'))" works as expected ;-)
    >>> 
    >>> 
    >>> ????? Comments?  ????? Thanks for your valuable work in
    >>> making it easier for people everywhere to do quality
    >>> statistics.
    >> 
    >> The help page ?plot.table says that ylim defaults to c(0,
    >> max(x)), i.e.  c(0,3) in your example.? If you're asking
    >> to plot that on a log scale, there are bound to be
    >> problems.
    >> 
    >> If you specify ylim, e.g. as c(min(tstTable),
    >> max(tstTable)), things are fine in your example; they
    >> won't be in examples where the min is zero.
    >> 
    >> Duncan Murdoch

    > 	  Thanks.  I looked at the help file but didn't read it
    > carefully enough.

    > 	  Spencer

If you have a table with  0  counts  and think you'd prefer
log="y" --- something I strongly agree is often a good idea,
giving much more useful plots --- 

I'd consider in this case using the good old  
   log( 1+   y )
or log( eps+ y )  trick.

My colleague Werner Stahel has spent quite a bit of effort in
order to make such "log-transformed plots in case of {zero etc}"
plot even smarter and convenient...
and has put this (and many more related ideas of doing smart and
robust good data analysis) in his package 'plgraphics'
(on R-forge, but still not on CRAN unfortunately).
With many thanks to Ian Howson, still nicely available also here:

    https://rdrr.io/rforge/plgraphics/

His generalized  log(1 + y)   is  plgraphics::logst(),
documented on the rdrr mirror here
  https://rdrr.io/rforge/plgraphics/man/logst.html

Martin

  
  


  


      

    

    

      
      

        


  

        

      Bill Dunlap
    

    

      
      #
    

  


  

      
Martin wrote

If you have a table with  0  counts  and think you'd prefer
log="y" --- something I strongly agree is often a good idea,
giving much more useful plots ---

I'd consider in this case using the good old
   log( 1+   y )
or log( eps+ y )  trick.


One could also sqrt(y), which helps stabilize the variances of count data.

Making nicely spaced and labelled tick marks for these transformations can
be a pain.  Perhaps some package already does this.

-Bill

On Mon, May 30, 2022 at 3:41 AM Martin Maechler <maechler at stat.math.ethz.ch>
wrote:

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Martin Maechler
    

    

      
      #
    

  


  

          

      
      
      
    

        
> Martin wrote

    > If you have a table with  0  counts  and think you'd prefer
    > log="y" --- something I strongly agree is often a good idea,
    > giving much more useful plots ---

    > I'd consider in this case using the good old
    > log( 1+   y )
    > or log( eps+ y )  trick.


    > One could also sqrt(y), which helps stabilize the variances of count data.

Definitely,  thank you, Bill!

What I mean above (and I think you understood, but probably not
many other readers because I was too terse), 
was of course to use   log="y"  with the "+ eps" trick,
i.e., {in a general situation}

      plot(x, y+eps, log="y")

so the labels show numbers on the y+eps scale, and for smallish
eps, this is visually the same as y-scale - unless you are close to y=0.


    > Making nicely spaced and labelled tick marks for these transformations can
    > be a pain.  Perhaps some package already does this.

    > -Bill

Not used yet, but from documentation, Stahel's 'plgraphics'
package (see bottom below),  does allow "arbitrary" transformation.

For the specific case of table() {or xtable()} results with true counts,
I agree it would be nice to have something like  'sqrt="y"' or
just 'sqrt=TRUE' which would "show" sqrt(<count>) but label the
axis non-equidistantly with counts.

A bit like

   y <- sort(rlnorm(333, 3))
   plot(qnorm(ppoints(y)), y, log="y", yaxt="n")
   sfsmisc::eaxis(2, sub=1)

does for log-transformed.

The simple traditional-graphics    plot(*, log="y") is often
good enough, but I like to see from the ticks that there was a
transformation.

Martin

    > On Mon, May 30, 2022 at 3:41 AM Martin Maechler <maechler at stat.math.ethz.ch>

        
> wrote:

        
>> >>>>> Spencer Graves
    >> >>>>>     on Sat, 28 May 2022 11:41:49 -0500 writes:
    >>

        
>> > On 5/28/22 11:23 AM, Duncan Murdoch wrote:

        
>> >> On 28/05/2022 11:33 a.m., Spencer Graves wrote:

        
>> >>> Dear R Developers:
    >> >>>
    >> >>>
    >> >>>       Consider the following example:
    >> >>>
    >> >>>
    >> >>> (tstTable <- table(rep(1:3, 3:1))) plot(tstTable)
    >> >>> plot(tstTable, log='y')
    >> >>>
    >> >>>
    >> >>>       "plot(tstTable)" works as expected.
    >> >>> "plot(tstTable, log='y')" gives a warning:
    >> >>>
    >> >>>
    >> >>> Warning message: In plot.window(...) :     nonfinite
    >> >>> axis=2 limits [GScale(-inf,0.477121,..); log=TRUE] --
    >> >>> corrected now
    >> >>>
    >> >>>
    >> >>>       AND the plot has a y axis scale running from
    >> >>> 1e-307 to 1e+13.
    >> >>>
    >> >>>
    >> >>>       This is with R 4.2.0 (R Console and the current
    >> >>> RStudio) under macOS 11.6.6.
    >> >>>
    >> >>>
    >> >>>       "plot(as.numeric(names(tstTable),
    >> >>> as.numeric(tstTable), log='y'))" works as expected ;-)
    >> >>>
    >> >>>
    >> >>>       Comments?        Thanks for your valuable work in
    >> >>> making it easier for people everywhere to do quality
    >> >>> statistics.
    >> >>
    >> >> The help page ?plot.table says that ylim defaults to c(0,
    >> >> max(x)), i.e.  c(0,3) in your example.  If you're asking
    >> >> to plot that on a log scale, there are bound to be
    >> >> problems.
    >> >>
    >> >> If you specify ylim, e.g. as c(min(tstTable),
    >> >> max(tstTable)), things are fine in your example; they
    >> >> won't be in examples where the min is zero.
    >> >>
    >> >> Duncan Murdoch
    >> 
    >> >     Thanks.  I looked at the help file but didn't read it
    >> > carefully enough.
    >> 
    >> >     Spencer
    >> 
    >> If you have a table with  0  counts  and think you'd prefer
    >> log="y" --- something I strongly agree is often a good idea,
    >> giving much more useful plots ---
    >> 
    >> I'd consider in this case using the good old
    >> log( 1+   y )
    >> or log( eps+ y )  trick.
    >> 
    >> My colleague Werner Stahel has spent quite a bit of effort in
    >> order to make such "log-transformed plots in case of {zero etc}"
    >> plot even smarter and convenient...
    >> and has put this (and many more related ideas of doing smart and
    >> robust good data analysis) in his package 'plgraphics'
    >> (on R-forge, but still not on CRAN unfortunately).
    >> With many thanks to Ian Howson, still nicely available also here:
    >> 
    >> https://rdrr.io/rforge/plgraphics/
    >> 
    >> His generalized  log(1 + y)   is  plgraphics::logst(),
    >> documented on the rdrr mirror here
    >> https://rdrr.io/rforge/plgraphics/man/logst.html
    >> 
    >> Martin