Re: [R] heatmap on pre-established hclust output?

From: Gregory. R. Warnes <greg_at_warnes.net>
Date: Mon, 19 May 2008 15:17:02 -0400

Try this:

 > library(gplots)
 > x <- as.matrix(USArrests)
 > hc <- hclust(dist(USArrests), "ave")
 > dend1 <- as.dendrogram(hc)
 > heatmap.2(x, Rowv=dend1)

-G

On May 16, 2008, at 12:23PM , Jeremiah Rounds wrote:

>
> > To: r-help@stat.math.ethz.ch> From: johannes_graumann@web.de>
> Date: Fri, 16 May 2008 17:55:26 +0200> Subject: [R] heatmap on pre-
> established hclust output?> > Hi,> > Can someone please guide me
> towards how to produce "heatmap" output from the> output of
> "hclust" run prior to the actual "heatmap" call? I have some>
> rather lengthy clustering going on and tweeking the visual output>
> with "heatmap" recalculating the clustering every time is not
> feasible.> > Thanks, Joh
>
> I can't say that i have actually tackled this, but I have some
> experience with the functions you mentioned. Heatmap takes an
> hclustfun function parameter. You can create a custom clustering
> function. I don't believe there is a rule that says you have to do
> actual work in that function call. Look at just returning the
> results of your more complicated clustering in that call without
> actually doing the calculations.
>
> Jeremiah Rounds
> Graduate Student
> Utah State University
>
> > > ______________________________________________> R-help_at_r-
> project.org mailing list> https://stat.ethz.ch/mailman/listinfo/r-
> help> PLEASE do read the posting guide http://www.R-project.org/
> posting-guide.html> and provide commented, minimal, self-contained,
> reproducible code.
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Gregory R. Warnes, Ph.D.
Associate Professor
Center for Biodefence Immune Modeling

    and
Department of Biostatistics and Computational Biology University of Rochester

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