[BioC] heatmap genenames

[Sean Davis]

If I remember correctly, heatmap does reorder the genes with respect to 
the dendrogram (not with R right now).  Try using heatmap( ....., 
rowV=1:n) where n is the number of genes.  Also, check the 
capitalization for rowV.

Sean

On Nov 4, 2004, at 12:03 PM, Claire Wilson wrote:

>
> Hello,
>
> Many thanks for your reply, I have tried repeating the clustering done
> by heatmap using hclust to obtain the row order as follows:
>
> d <- dist(mydata)
> hc.d <- hclust(d)
> gene.order <- hc.d$order
>
> and compared the order to what I see on a heatmap when I do
>
> heatmap(mydata)
>
> However, it would appear that the ordering of genes within a heatmap
> made from heatmap(mydata) is different to that seen if a dendrogram is
> made from from hc.d. So I am thinking something else happens after 
> doing
> the hierarchical clustering within the heatmap function, but I have so
> far been unsuccessful in my attempts to try and work out what it is.
>
> Claire
>
>
>> Dear Claire,
>>
>> if I remember well heatmap uses hclust as default clustering
>> function with
>> distances given by "dist" that, in turn, uses "euclidean"
>> distance as default.
>>
>> So, I guess that you should be able to obtain the desired
>> order easily runing
>>
>> hclust(dist( your.data ))$order
>>
>> or something like
>>
>> my.cluster<-hclust(dist( my.data ))
>> rownames( my.data )[my.cluster$order]
>>
>>
>> Let me know if it works
>> Alessandro
>>
>>
>> At 15.06 04/11/2004, you wrote:
>>> Dear all,
>>>
>>> I have been using the heatmap function to visualise my data and would
>>> like to obtain a list of my genes in the same order that
>> they appear in
>>> the heatmap. I have looked through the mail archives and tried just
>>> creating a dendogram and using order.dendogram but have so far been
>>> unsuccessful. Can anyone point me in the right direction?
>>>
>>> cheers
>>>
>>> claire
>>>
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>>
>>
>
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