Hi Wolfgang,

I plot it on my screen in a x11 device. In that case it's extremely slow.
But you can NOT distinguish the leaves. Of course.

Creating this image through bmp(...) allows me to plot the tree in a much
shorter time.

Tony

On 15 April 2010 00:14, Wolfgang Huber <whuber@embl.de> wrote:

>
> Hi Anthony
>
> just out of interest, what graphics device are you using to view the
> heatmap with 8000 rows and the tree with 8000 branches?
>
> I wonder because if you will spend 1 mm per row, 8000 rows are 8 metres
> [that's 4 centiinch and 26.2 feet in the US].
>
>        Best wishes
>           Wolfgang
>
>
> Anthony Ferrari ha scritto:
>
>> Hi all,
>>
>> I have got a 8000*200 gene expression matrix. I am clustering rows and
>> columns with hclust.
>>
>> I want to plot something like generated by 'heatmap' which means an
>> heatmap
>> with corresponding array and gene trees. So, the fact is that the gene
>> tree
>> should be horizontal.
>>
>> With 'plot' function applied to an hclust object, the dendrogram is always
>> vertical. But plotting the tree is really fast.
>>
>> To plot the gene tree horizontal, I saw that coercing the hclust object
>> with
>> as.dendrogram allows one to use the option horiz=TRUE in 'plot'. That's
>> pretty true but plotting the dendrogram for 8000 genes requires then an
>> infinity of time. I see each branch of the tree be slowly drawn one by
>> one.
>>
>> Why this difference in calculation time ?
>> And is there a way to plot a horizontal tree as quick as
>> 'plot(hclust_object,...)' does ?
>>
>>
>> best regards,
>>
>> tony
>>
>>        [[alternative HTML version deleted]]
>>
>>
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>>
>
> --
>
>
> Wolfgang Huber
> EMBL
> http://www.embl.de/research/units/genome_biology/huber
>
>
>

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