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

[Jason Shoemaker]

This previous discussion seems to answer the probleb:
https://stat.ethz.ch/pipermail/bioconductor/2009-July/028898.html
Jason

On Fri, Apr 15, 2011 at 11:48 AM, Saurin D. Jani <saurin_jani at yahoo.com> wrote:
> Hi Sean,
>
> Thanks for your reply. I tried all those..options in arguments. When I do Rowv = FALSE.. column clustering is not there.
>
> thats the reason I got confused..!!
>
> heatmap.2(FeatureX,col=bluered,Colv = as.dendrogram(hclust(col.dist, method = "centroid")), dendrogram = "column", scale = "none",key = TRUE, Rowv = FALSE, density.info = "none",tracecol="black");
>
>
> 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, 10:45 PM
>> 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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>> >
>>
>
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-- 
Jason Shoemaker, Ph D
Japanese Science and Technology Agency
Infection Induced Host Response Laboratory
The Institute of Medical Science,
University of Tokyo