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

[Jason Shoemaker]

I suspect the problem is the Colv call. If I understand this
correctly, Colv only accepts only T or F arguments. When that is
erased it seems to work just fine. Try using the hclustfun option
instead of calling Colv = as.dendrogram(hclust(col.dist, method =
"centroid")). I am not sure how to change the parameters of hclust
though.
Cheers
Jason

On Fri, Apr 15, 2011 at 11:31 AM, Saurin D. Jani <saurin_jani at yahoo.com> wrote:
>
> 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
>
>
>
>
>



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