Re: [Rd] error in plot.dendrogram (PR#7300)

From: <wolski_at_molgen.mpg.de>
Date: Fri 22 Oct 2004 - 00:52:41 EST


Hi,

First. If you should not do it like you write here. You will get an error loading the rda file. It is a binary format.

Error in load(dFile) : input has been corrupted, with LF replaced by CR

Hence, you should specify mode="wb" for downloading binary formats.

Try this code.

file.remove("hres.rda")

dFile <- paste(getwd(),"/hres.rda",sep="") if(!file.exists(dFile))

    download.file(url ="http://www.molgen.mpg.de/~wolski/hres.rda", dest= dFile,mode="wb") load(dFile)

hresd
plot(hresd)

In one think you are right, the X axis. But there is an ERROR.

On my Machine (see previous mail) not the complete dendrogram is drawn. It just draws the first 100 leavs out of 380 when I run Second. Even if I increase the size of the window maximally the dendrogram is not plotted.
And I checked it just again on a linux box. And it does not work there either.

How the dendrogram should look like you can figure out looking at the following.

hclustObj <- paste(getwd(),"/hress.rda",sep="") if(!file.exists(dFile))

    download.file(url ="http://www.molgen.mpg.de/~wolski/hress.rda", dest= hclustObj ,mode="wb") load(dFile)

hress
plot(hress)

hressd<-as.dendrogram(hress)
plot(hressd)

Third. I have expected this comment about if it is meaningfull or not.  First for what I need it is it meaningfull. Second it is a valid dendrogram generated by as.dendrogram from a vaild hclust object. I do not need a plot routine which teaches me what she thinks is meaningfull or not.

/E

Martin Maechler wrote:

>>>>>>"Eryk" == Eryk Wolski <wolski@molgen.mpg.de>
>>>>>> on Thu, 21 Oct 2004 13:41:29 +0200 (CEST) writes:
>>>>>>
>>>>>>
>
> Eryk> Hi,
>
> Eryk> hres <- hclust(smatr,method="single")
> Eryk> hresd<-as.dendrogram(hres)
> Eryk> as.dendrogram(hres)
> Eryk> `dendrogram' with 2 branches and 380 members total, at height 2514.513
> Eryk> plot(hresd,leaflab="none") #<-error here.
>
>definitely no error here.. maybe your graphic window is too
>small or otherwise unable to show all the leaf labels?
>
> Eryk> #the plotted dendrogram is incomplete. The x axis is not drawn.
>
>ha! and why should this be a bug????
>Have you RTFHP and looked at its example??
>There's never an x-axis in such a plot!
>
>[You really don't want an x-axis overlayed over all the labels]
>
> Eryk> #The interested reader can download the
>
> Eryk> save(hresd,file="hres.rda")
>
> Eryk> #from the following loacation
> Eryk> www.molgen.mpg.de/~wolski/hres.rda
>
>If you send a bug report (and please rather don't..),
>it should be reproducible, i.e., I've just wasted my time for
>
>dFile <- "/u/maechler/R/MM/Pkg-ex/stats/wolski-hres.rda"
>if(!file.exists(dFile))
> download.file(url ="http://www.molgen.mpg.de/~wolski/hres.rda", dest= dFile)
>load(dFile)
>hresd
>plot(hresd)
>
>----
>
>If you look at this plot I hope you rather see that "single" has
>been an extremly unuseful clustering method for this data / dissimilarities,
>and you'd rather tried other methods than to which for an
>x-axis.
>
>If you really want one (just to see that it doesn't make sense),
>you can always add
> axis(1, fg = "red")
>
>Martin
>
>
>

-- 
Dipl. bio-chem. Witold Eryk Wolski
MPI-Moleculare Genetic
Ihnestrasse 63-73 14195 Berlin
tel: 0049-30-83875219                 __("<    _
http://www.molgen.mpg.de/~wolski      \__/    'v'
http://r4proteomics.sourceforge.net    ||    /   \
mail: witek96@users.sourceforge.net    ^^     m m
      wolski@molgen.mpg.de

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Received on Fri Oct 22 05:34:34 2004

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