[BioC] Help on hclust function

[Björn Usadel]

Hi,

as stated already this is nearly impossible to visualize as a 
dendrogramm. But you might want to export your data in newick format, I 
guess it was something like hc2newick or so package "ctc".
Then you can visualize the data using standard/specialized treeviewing 
programs, to explore your trees.
But I guess it will be hard to make sense out of such large trees by eye.

Cheers,
björn

> Hello everybody,
>
> I am using the hclust()  function in R.
> I have a 2000*12 matrix of expression data.
> I have created a distance matrix with dist() using Euclidean method.
> Then in hclust I have used complete linkage method.
> Now when I am trying to plot the dendogram with pclust method I cannot 
> see the details of the tree.
> The gene names and the lower parts of the dendogram are not visible
> Is there any method by which I can see only selected parts of the 
> dendogram.....or Zoom in or out....
> I have used the follwing command for pclust:
> plclust(H2000, unit = FALSE, level = FALSE, hmin = 0,
> +              square = TRUE, labels =names2000 , plot. = TRUE,
> +              axes = TRUE, frame.plot = FALSE, ann = TRUE,
> +              main = "", sub = NULL, xlab = NULL, ylab = "Height")
>
> I am attaching a snapshot of the dendogram that I am getting.
> Please help ASAP.
>
> Thanks in advance,
> Madhurima.
>
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