[BioC] row clustering in heatmap.2

Johnstone, Alice Alice.Johnstone at esr.cri.nz
Thu Jun 26 01:59:03 CEST 2008

Ahh thanks for your reply Mark,
I had atempted this yesterday using row means of the treatment.. but was
of course still getting a mix of up and down as I wasn't accounting for
the expression level in the control.  
Looks great now.

-----Original Message-----
From: Mark Cowley [mailto:m.cowley0 at gmail.com] 
Sent: Wednesday, 25 June 2008 8:12 p.m.
To: Johnstone, Alice
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] row clustering in heatmap.2

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



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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