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

[Jason Shoemaker]

hmm. I am not sure what else to try then. I followed that example, ran
this code:
> hclust2 <- function(x, method="average", ...)
+   hclust(x, method=method, ...)
> dist2 <- function(x, ...)
+   as.dist(1-cor(t(x), method="pearson"))
heatmap.2(Rowv=F,as.matrix(mtcars), distfun=dist2, hclustfun=hclust2)

it seems to run fine...I attached the figure here. Hopefully someone
else knows the solution.
Goodluck!
Jason




On Fri, Apr 15, 2011 at 12:12 PM, Saurin D. Jani <saurin_jani at yahoo.com> wrote:
> 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
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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
>>
>



-- 
Jason Shoemaker, Ph D
Japanese Science and Technology Agency
Infection Induced Host Response Laboratory
The Institute of Medical Science,
University of Tokyo
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