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 <[EMAIL PROTECTED]>
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: [EMAIL PROTECTED] ^^ m m
[EMAIL PROTECTED]______________________________________________ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
