[BioC] row clustering in heatmap.2

[Mark Cowley]

Hi Alice,
 From the help page (?heatmap.2):
    Rowv: determines if and how the _row_ dendrogram should be
          reordered.  By default, it is TRUE, which implies dendrogram
          is computed and reordered based on row means. If NULL or
          FALSE, then no dendrogram is computed and reordering is done.
          If a 'dendrogram', then it is used "as-is", ie without any
          reordering. If a vector of integers, then dendrogram is
          computed and reordered based on the order of the vector.

1) reorder the rows before you put it into the heatmap.2
	see ?order
2) turn row-reordering off in the heatmap by using heatmap.2 with  
Rowv=FALSE, Colv=TRUE, dendrogram="column" if you want the columns  
reordered, or
Rowv=FALSE, Colv=FALSE, dendrogram="none" for neither row or column  
dendrograms

cheers,

mark

On 25/06/2008, at 12:49 PM, Johnstone, Alice wrote:

> Hi
> Im having a hard time trying to understand the clustering functions  
> used
> with heatmap.2.  I have expression data, treatment vs control for  
> which
> I have created a heatmap for (default arguments).  But I want to  
> reorder
> the rows so that the row with the highest expression in my treatment  
> is
> at the top, the 2nd having the 2nd highest expression..etc.. down to  
> the
> last row having the lowest expression (compared to the control).
> Any suggestions on how I can go about this would be very much
> appreciated!
> Thank you
>
> Alice Johnstone
>
> PhD Student
> Institute of Environmental Science and Research Ltd
> Kenepuru Science Centre
> 34 Kenepuru Drive
> PO Box 50-348
> Porirua
> New Zealand
>
> Tel:  + 64 4 914-0717
> Fax: + 64 4 914-0770
>
>
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