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

[Saurin D. Jani]

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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> >
>