[R] plot.dendrogram and plot.hclust ZOOM into the height?

2004-10-19 Thread Witold Eryk Wolski
Hi,
I clustered a distance matrix and would like to draw it using 
plot.hclust or plot.dendrogram.
The dendrogram is not informative because I have a few extremely small 
dissimilarities in the distance matrix (e.g. 0), but most of the other 
distances are in the range 1e10+-5000.
I would like to show the tree only for the height of 1e10+-5000 but 
unfortunately their are no parameter like xlim,ylim in the function?
Are there other ways to ZOOM?

Any suggestions?
/E
--
Dipl. bio-chem. Witold Eryk Wolski
MPI-Moleculare Genetic
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[R] plot.dendrogram

2004-09-08 Thread Marta Rufino
Dear R-users,

I would like to change the labels size and format in the node ends of a dendrogram, 
how can I do it?
How can I use different symbols/colors in each node ends ?


I manage to do it with plot.cluster, but heat map uses plot.dendrogram.


Can anyone help me please?
thank you
Marta


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Re: [R] plot.dendrogram

2004-09-08 Thread Adaikalavan Ramasamy
Try setting something like cex=0.5 in the plot. It works for at least
hclust. Here is a quick example using hclust to show how you can get
away with set the colours.

data(USArrests)
hc - hclust(dist(USArrests), ave)

plot(hc, hang=-1, cex=0.5)
labels - rownames(USArrests)[ hc$order]; n - length(labels)
mtext(labels, side=1, at=1:n, las=2, col=1:n, cex=0.5, line=0)

If you want to get rid of the double labelling (which is useful for
checking), then set labels=FALSE in the plot().


The trick now becomes how to generalise this to other dendrogram and
when hang=-1 is not the case. 

My initial though was to look into plot.hclust to see how the coordinate
for label placement was calculated and replace it with text(...,
col=col.label). But it appears that this is done with a .Internal
function and I have not learned how to read/edit this yet.




On Wed, 2004-09-08 at 11:06, Marta Rufino wrote:
 Dear R-users,
 
 I would like to change the labels size and format in the node ends of a dendrogram, 
 how can I do it?
 How can I use different symbols/colors in each node ends ?
 
 
 I manage to do it with plot.cluster, but heat map uses plot.dendrogram.
 
 
 Can anyone help me please?
 thank you
 Marta
 
 
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 https://stat.ethz.ch/mailman/listinfo/r-help
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