[R] heatmap help

[Liaw, Andy]

Sorry.  I think you need the argument distfun=as.dist.  E.g.,

heatmap(x, distfun=as.dist, symm=TRUE, scale="none")

Andy

> From: Liaw, Andy
> 
> I believe you want to pass the (symmetric) matrix as is, 
> rather than wrapped
> in as.dist().  E.g.,
> 
> x <- as.matrix(dist(matrix(rnorm(100), 20, 5)))
> heatmap(x, symm=TRUE, scale="none")
> 
> HTH,
> Andy
> 
> > From: Paul Lepp
> > 
> > Dear R wizards,
> > 	Hopeful someone can help me with what I believe is a 
> > pretty simple task.  I
> > pretty new to R so some (much) of the obvious escapes me. How 
> > do I get a
> > distance matrix into heatmap?  What do I tell distfun if what 
> > I'm trying to
> > map is already an ordered distance matrix?  I tried >heatmap(x,
> > distfun=as.dist(x)) where x is the distance matrix but R gave 
> > me an error.
> > Thanks in advance for any help.
> > 
> > Paul Lepp
> > 
> >  `-:-.   ,-;"`-:-.   ,-;"`-:-.   ,-;"`-:-.   ,-;"`-:-.   ,-;"`-:-.
> >    `=`,'=/     `=`,'=/     `=`,'=/     `=`,'=/     `=`,'=/     `=`
> >      >==/        >==/        >==/        >==/        >==/
> >    ,=,-<=`.    ,=,-<=`.    ,=,-<=`.    ,=,-<=`.    ,=,-<=`.    ,=,
> > ,-'-'   `-=_,-'-'   `-=_,-'-'   `-=_,-'-'   `-=_,-'-'   `-=_,-'-'
> > Paul Lepp, Ph.D.                       Stanford School of Medicine
> > 
> > VAPAHCS, 154T                   Dept. of Microbiology & Immunology
> > 3801 Miranda Ave                               Stanford University
> > Palo Alto, CA 94304                                   Stanford, CA
> > (650) 493-5000 x66762		               fax: 
> (650) 852-3291
> > http://cmgm.stanford.edu/~pwlepp          pwlepp at cmgm.stanford.edu
> > 
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> >
> 
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