[BioC] Fwd: heatmap.2 question

[Steve Lianoglou]

Also: Someone correct me if I'm wrong, as I often turn myself around
on this one, but also note that the y-axis you see on the heatmap.2 is
"flipped." So the "first" row (`result$rowInd[1]`) is at the bottom of
the heatmap, not the top.

-steve

On Thu, May 24, 2012 at 11:18 AM, James W. MacDonald <jmacdon at uw.edu> wrote:
> Hi Alyaa,
>
>
> On 5/24/2012 11:04 AM, Alyaa Mahmoud wrote:
>>
>> Hi All
>>
>> How can I possibly extract the clusters by rows from a heatmap generated
>> by
>> heatmap.2 function. i.e. the heatmap is generated with colouring for every
>> cluster of rows and I want to retrieve the members of each cluster.
>
>
> Note that heatmap.2() uses hclust() to create the clusters. There is a
> function cutree() that can be used to get the groups from the output of
> hclust().
>
> Also note that heatmap.2() invisibly returns a list that includes both the
> row and column dendrograms (by returning the list invisibly, you don't get a
> bunch of junk printed out to your console. However, if you use the
> assignment function (<-) to assign the output to an object, you can then
> extract whichever dendrogram you want.).
>
> Best,
>
> Jim
>
>
>
>>
>>
>> Any clue would be much appreciated
>>
>> Thank you very much
>> Alyaa
>>
>> KAUST/AUC Marine Genomics Project
>> American University in Cairo
>> Egypt
>> 2918
>>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
>
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-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact