Hi Jason, Sean, Thank you so much for your time and reply. I really appreciate that. Now, it does work. The only explanation I have it...when I fixed my strings for input sample names..I got it working..as Jason showed. have a fantastic weekend, Thanks, Saurin --- On Fri, 4/15/11, 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: Friday, April 15, 2011, 12:42 AM > 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 > >> > 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 > >> > > > > > > -- > Jason Shoemaker, Ph D > Japanese Science and Technology Agency > Infection Induced Host Response Laboratory > The Institute of Medical Science, > University of Tokyo >