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

[Saurin D. Jani]

Hi Jason,

Thanks. but, somehow that does not work..!

hclust2 <- function(x, method="average")
dist2 <- function(x)
  as.dist(1-cor(t(x), method="pearson"))

heatmap.2(FeatureX, distfun=dist2, hclustfun=hclust2);

Error in UseMethod("as.dendrogram") : 
  no applicable method for 'as.dendrogram' applied to an object of class "function"


## one small experiment:

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");


I suspect that...my column names are bit different in length...when I tried with "AA_0001" and so on..above heatmap.2 call works exactly what I want...!! 

Did any one experienced similar ? this is just me..!

Thanks,
Saurin

--- On Thu, 4/14/11, Jason Shoemaker <jshoe at ims.u-tokyo.ac.jp> wrote:

> From: Jason Shoemaker <jshoe at ims.u-tokyo.ac.jp>
> Subject: Re: [BioC] heatmap.2 ..help..how to cluster column ..but not Rows..
> To: "saurin_jani" <saurin_jani at yahoo.com>
> Cc: "Sean Davis" <sdavis2 at mail.nih.gov>, "Bioconductor Bioconductor" <bioconductor at stat.math.ethz.ch>
> Date: Thursday, April 14, 2011, 11:01 PM
> 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
> >> >> >
> >> >> >
> >> _______________________________________________
> >> >> > Bioconductor mailing list
> >> >> > Bioconductor at r-project.org
> >> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> >> > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> >> >> >
> >> >>
> >> >
> >> >
> _______________________________________________
> >> > Bioconductor mailing list
> >> > Bioconductor at r-project.org
> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> >> >
> >>
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
> 
> 
> 
> -- 
> Jason Shoemaker, Ph D
> Japanese Science and Technology Agency
> Infection Induced Host Response Laboratory
> The Institute of Medical Science,
> University of Tokyo
>