R help - Feb 2011 - heatmap-how to change the order of the rows (genes)

Hi,

I have a question about the heatmap dendrogram in R.  I loaded my data
matrix in command heatmap(), and it gave me a heatmap accordingly, and the
rows (genes) also were clustered accordingly.  But now I don't want the
genes clustered in that way, I have a new order of these genes, and want the
rows of the heatmap are drawed as the order I give.  Could anybody help me
on that?  Thank you!

Yan

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Hi,

On Wed, Feb 9, 2011 at 12:18 PM, yan liu <yanliusun at gmail.com>
wrote:
> Hi,
>
> I have a question about the heatmap dendrogram in R. ?I loaded my data
> matrix in command heatmap(), and it gave me a heatmap accordingly, and the
> rows (genes) also were clustered accordingly. ?But now I don't want the
> genes clustered in that way, I have a new order of these genes, and want
the
> rows of the heatmap are drawed as the order I give. ?Could anybody help me
> on that? ?Thank you!
Check out the docs for heatmap a bit more carefully:

R> ?heatmap

I would try setting Rowv=NA, and reorder the rows of your matrix as
you want them to be ordered, ie:

R> heatmap(m[my.gene.order,], Rowv=NA, ...)

Or something like that.

-- 
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

----------------------------------------
> Date: Wed, 9 Feb 2011 12:18:57 -0500
> From: yanliusun at gmail.com
> To: r-help at r-project.org
> Subject: [R] heatmap-how to change the order of the rows (genes)
>
> Hi,
>
> I have a question about the heatmap dendrogram in R. I loaded my data
> matrix in command heatmap(), and it gave me a heatmap accordingly, and the
> rows (genes) also were clustered accordingly. But now I don't want the
> genes clustered in that way, I have a new order of these genes, and want
the
> rows of the heatmap are drawed as the order I give. Could anybody help me
[[elided Hotmail spam]]
>


?heatmap 

Rowv=NA 
or
Colv=NA

but first time I tried this something didn't work but
I think eventually it did work for me with both, not sure
if you have problem with one only.


> Yan
>
> [[alternative HTML version deleted]]
>
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