Thanks to all of you, this was really helpful :)

Alyaa

On Thu, May 24, 2012 at 6:42 PM, James W. MacDonald <jmacdon@uw.edu> wrote:

> Yep. The heatmap itself is created using image(), which plots the matrix
> from the bottom up, so the [1,1] position of the matrix is at the lower
> left of the image.
>
>
> Best,
>
> Jim
>
>
> On 5/24/2012 11:29 AM, Steve Lianoglou wrote:
>
>> 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@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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>>>
>>
>>
>>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
>


-- 
Alyaa Mahmoud

"Love all, trust a few, do wrong to none"- Shakespeare

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