[BioC] heatmap.2 ..help..how to cluster column ..but not Rows..

[Sean Davis]

On Thu, Apr 14, 2011 at 10:34 PM, Saurin D. Jani <saurin_jani at yahoo.com> wrote:
> Hi Sean,
>
> heatmap.2(FeatureX,col=bluered,Colv = as.dendrogram(hclust(col.dist, method = "centroid")), scale = "none",key = TRUE, dendrogram = "column", density.info = "none",tracecol="black");
>
>
> This one gives dendrogram on column and key is there as well..the only problem is Rows are being clustered as well...how do I prevent rows to get clustered?
>

Take a look at the Rowv argument; Rowv=FALSE is probably what you want.

Sean


> Thanks,
> Saurin
>
>
>
> --- On Thu, 4/14/11, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>
>> From: Sean Davis <sdavis2 at mail.nih.gov>
>> Subject: Re: [BioC] heatmap.2 ..help..how to cluster column ..but not Rows..
>> To: saurin_jani at yahoo.com
>> Cc: "Bioconductor Bioconductor" <bioconductor at stat.math.ethz.ch>
>> Date: Thursday, April 14, 2011, 10:24 PM
>> On Thu, Apr 14, 2011 at 9:49 PM,
>> Saurin D. Jani <saurin_jani at yahoo.com>
>> wrote:
>> > Hi BioC,
>> >
>> > This must be simple but somehow I can not be able to
>> do it...
>> > How can I cluster samples only.. below code is giving
>> me dendrogram on both rows and clumns...! if I do Rowv =
>> FALSE..then I don't see any colors and KEY.
>> >
>>
>> Hi, Saurin.
>>
>> See the "dendrogram" argument in heatmap.2 help.  In
>> particular,
>> dendrogram="column" will turn off the row dendrogram.
>>
>> Sean
>>
>> > Please see this:
>> >
>> > FeatureX is Matrix with proper rows and colmns.
>> >
>> >
>> > row.dist <- as.dist(1 - cor(t(FeatureX)));
>> > col.dist <- as.dist(1 - cor(FeatureX));
>> > heatmap.2(FeatureX,col=bluered,Colv =
>> as.dendrogram(hclust(col.dist, method = "centroid")), scale
>> = "none",key = TRUE,density.info =
>> "none",tracecol="black");
>> >
>> > Thank you in advance,
>> > Saurin
>> >
>> > _______________________________________________
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>> >
>>
>
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