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

[Saurin D. Jani]

Hi Jason,

I tried Rowv = "none"

heatmap.2(FeatureX,col=bluered,Colv = as.dendrogram(hclust(col.dist, method = "centroid")), scale = "none",key = TRUE, Rowv = "none", density.info = "none",tracecol="black");

Warning message:
In heatmap.2(FeatureX, col = bluered, Colv = as.dendrogram(hclust(col.dist,  :
  Discrepancy: Rowv is FALSE, while dendrogram is `both'. Omitting row dendogram.
Error in plot(ddr, horiz = TRUE, axes = FALSE, yaxs = "i", leaflab = "none") : 
  error in evaluating the argument 'x' in selecting a method for function 'plot'


Still I don't get columns clustered and key is not there.

Any thoughts? 

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: "Bioconductor Bioconductor" <bioconductor at stat.math.ethz.ch>
Date: Thursday, April 14, 2011, 10:12 PM

Set Rowv="none"

You will get a warning because of the dendrogram parameters. You can adjust those accordingly
Cheers
Jason

On Fri, Apr 15, 2011 at 10:49 AM, 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.



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