R help - Jan 2001 - Is ther a possibility to display the log(frequency) instead of the frequency in the hist plot?

Is there a possibility to display the log(frequency) instead of the
frequency in the hist?
--
Witold Eryk Wolski
Max Plank Institut fuer Molekulare Genetik
Ihnestr73 14195 Berlin
Germany
tel.:
Work 0049-30-84131426
http://www.molgen.mpg.de/~wolski


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Witold Eryk Wolski wrote:
> 
>  Is there a possibility to display the log(frequency) instead of the
> frequency in the hist?
I think you want something like the following example:

 x <- runif(100) * 10
 my.hist <- hist(x)
 my.hist   # have a look at the values!
 my.hist$counts <- log(my.hist$counts, 10)  # logarithm with base 10
 plot(my.hist)  # now plot it again with log(frequency)


Uwe Ligges
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Uwe Ligges wrote:
> Witold Eryk Wolski wrote:
> >
> >  Is there a possibility to display the log(frequency) instead of the
> > frequency in the hist?
>
> I think you want something like the following example:
>
>  x <- runif(100) * 10
>  my.hist <- hist(x)
>  my.hist   # have a look at the values!
>  my.hist$counts <- log(my.hist$counts, 10)  # logarithm with base 10
>  plot(my.hist)  # now plot it again with log(frequency)
>
> Uwe Ligges
>
Hi Uwe!
First thanks for your answer.
Some questions still remain to me.
1. How take an log if one of the my.hist$counts equals 0?
2. You code expample produces an error message which i doesnt
understand.
> plot(my.hist)  # now plot it again with log(frequency)
Error in plot.window(xlim, ylim, log, asp, ...) :
        invalid xlim
3. I tried as workaround something similar.
plot(my.hist$mids,log(my.hist$counts),type="s") And this would work
quite good for
my needs.
But problem with log(0) = -Inf still remains.

I think I have to formulate my question more general. Why, and this is an
question
which I am asking myself since
I am started using  R becouse im using the hist plot quite often,  the hist plot
in
the base package has no similar
options like eg. the histogram plot in XMGR?


THX
Eryk


>
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--
Witold Eryk Wolski
Max Plank Institut fuer Molekulare Genetik
Ihnestr73 14195 Berlin
Germany
tel.:
Work 0049-30-84131426
http://www.molgen.mpg.de/~wolski


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Witold Eryk Wolski wrote:
> 
> Uwe Ligges wrote:
> 
> > Witold Eryk Wolski wrote:
> > >
> > >  Is there a possibility to display the log(frequency) instead of
the
> > > frequency in the hist?
> >
> > I think you want something like the following example:
> >
> >  x <- runif(100) * 10
> >  my.hist <- hist(x)
> >  my.hist   # have a look at the values!
> >  my.hist$counts <- log(my.hist$counts, 10)  # logarithm with base
10
> >  plot(my.hist)  # now plot it again with log(frequency)
> >
> > Uwe Ligges
> >
> 
> Hi Uwe!
> First thanks for your answer.
> Some questions still remain to me.
> 1. How take an log if one of the my.hist$counts equals 0?
You want to use a histogram, so you have to think about what you want to
do in that case.

> 2. You code expample produces an error message which i doesnt understand.
> > plot(my.hist)  # now plot it again with log(frequency)
> Error in plot.window(xlim, ylim, log, asp, ...) :
>         invalid xlim
??? 
No, cannot reproduce it with my example! 

> 3. I tried as workaround something similar.
> plot(my.hist$mids,log(my.hist$counts),type="s") And this would
work quite good for
> my needs.
> But problem with log(0) = -Inf still remains.
So we have to change the mathematical axioms. ;-)

> I think I have to formulate my question more general. Why, and this is an
question
> which I am asking myself since
> I am started using  R becouse im using the hist plot quite often,  the hist
plot in
> the base package has no similar
> options like eg. the histogram plot in XMGR?
> 
> THX
> Eryk
Uwe Ligges
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Witold Eryk Wolski skriver...
> Some questions still remain to me.
> 1. How take an log if one of the my.hist$counts equals 0?
log(my.hist$counts + 1)

-- 
Peter Kleiweg
http://www.let.rug.nl/~kleiweg/

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On Thu, 18 Jan 2001, Witold Eryk Wolski wrote:
> Uwe Ligges wrote:
>
> > Witold Eryk Wolski wrote:
> > >
> > >  Is there a possibility to display the log(frequency) instead of
the
> > > frequency in the hist?
> >
> > I think you want something like the following example:
> >
> >  x <- runif(100) * 10
> >  my.hist <- hist(x)
> >  my.hist   # have a look at the values!
> >  my.hist$counts <- log(my.hist$counts, 10)  # logarithm with base
10
> >  plot(my.hist)  # now plot it again with log(frequency)
> >
> > Uwe Ligges
> >
>
> Hi Uwe!
> First thanks for your answer.
> Some questions still remain to me.
> 1. How take an log if one of the my.hist$counts equals 0?
 You could try log10(my.hist$counts+1), which is a standard transformation
in ecology.
> 2. You code expample produces an error message which i doesnt understand.
> > plot(my.hist)  # now plot it again with log(frequency)
> Error in plot.window(xlim, ylim, log, asp, ...) :
>         invalid xlim
  I don''t get it here either.  Are you doing _exactly_ what Uwe
suggested
above?  Or are you doing the histogram etc. on your own data (rather than
a sample from runif())?  What is the range of your data?
> 3. I tried as workaround something similar.
> plot(my.hist$mids,log(my.hist$counts),type="s") And this would
work quite good for
> my needs.
> But problem with log(0) = -Inf still remains.
>
> I think I have to formulate my question more general. Why, and this is an
question
> which I am asking myself since
> I am started using  R becouse im using the hist plot quite often,  the hist
plot in
> the base package has no similar
> options like eg. the histogram plot in XMGR?
  What are those options?

  The general answers to the questions "why doesn''t R have ...
?" are
usually:

  1. it would be a useful feature, but no-one has thought of/suggested it
yet (?);
  2. ditto, but no-one has had the time or energy or specific knowledge
required to code it (e.g. full integration of 3D graphics, GAM);
  3. it represents something that at least some people (the R Core team,
who tend to be awfully knowledgeable about statistical and graphical
issues) think is a bad idea (e.g. type III sums of squares);
  4. it is minor enough, or there is an easy enough way to work around it,
that spending time on it/"bloating" R with it doesn''t seem
worthwhile.

  Ben

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I imagine that the point of logging the histogram count axis is just for
displaying purposes, and your suggestion would alter the scale.  I find it
easier to just leave the 0 counts as zero.

hist(my.data, plot=F)$counts -> my.hist.counts;
my.hist.counts[my.hist.counts != 0] <- 
                      log(my.hist.counts[my.hist.counts!= 0]);
plot(my.hist.counts, type="hist");


-Alex Morgan

Phone: 781-271-6306                       "They laughed at Newton.
Office: 3K-136                            They laughed at Einstein.
AOL Instant Messenger: HomeySage          But they also laughed at Groucho
                                          Marx."
                                                      --Carl Sagan

On Thu, 18 Jan 2001, Peter Kleiweg wrote:
> Witold Eryk Wolski skriver...
> 
> > Some questions still remain to me.
> > 1. How take an log if one of the my.hist$counts equals 0?
> 
> log(my.hist$counts + 1)
> 
> -- 
> Peter Kleiweg
> http://www.let.rug.nl/~kleiweg/
> 
>
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The only potential problem with this solution is that bins with zero
counts and bins with 1 count will both be treated as zeros.

  Consider:

my.data <- c(1.5,1.5,2.5,4.5,5.5,5.5)
my.hist.counts <- hist(my.data, plot=F, breaks=0:6)$counts

etc.

  This is an unlikely event with the default "breaks" settings,
though.  (On the other hand, the fact that you have bins with zero counts
says that you might well have bins with only 1 count.)

  Ben

On Thu, 18 Jan 2001, Alexander A. Morgan wrote:
> I imagine that the point of logging the histogram count axis is just for
> displaying purposes, and your suggestion would alter the scale.  I find it
> easier to just leave the 0 counts as zero.
>
> hist(my.data, plot=F)$counts -> my.hist.counts;
> my.hist.counts[my.hist.counts != 0] <-
>                       log(my.hist.counts[my.hist.counts!= 0]);
> plot(my.hist.counts, type="hist");
>
>
> -Alex Morgan
>
> Phone: 781-271-6306                       "They laughed at Newton.
> Office: 3K-136                            They laughed at Einstein.
> AOL Instant Messenger: HomeySage          But they also laughed at Groucho
>                                           Marx."
>                                                       --Carl Sagan
>
> On Thu, 18 Jan 2001, Peter Kleiweg wrote:
>
> > Witold Eryk Wolski skriver...
> >
> > > Some questions still remain to me.
> > > 1. How take an log if one of the my.hist$counts equals 0?
> >
> > log(my.hist$counts + 1)
> >
> > --
> > Peter Kleiweg
> > http://www.let.rug.nl/~kleiweg/
> >
> >
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> >
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> >
>
>
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-- 
318 Carr Hall                                bolker at zoo.ufl.edu
Zoology Department, University of Florida    http://www.zoo.ufl.edu/bolker
Box 118525                                   (ph)  352-392-5697
Gainesville, FL 32611-8525                   (fax) 352-392-3704

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