R help - Mar 2006 - Problems with heatmap.2 in the gregmisc package

Hi

Sorry to revisit an old problem, I seemed to solve this in 2004, only
for it to resurface :-S

I am trying to plot a heatmap, and I don't want the columns of my matrix
re-ordered.  The function doesn't seem to behave as the help would have
you believe:

a <- matrix(rnorm(100),nr=20)
a.d  <- dist(a)
a.hc <- hclust(a.d)
a.de <- as.dendrogram(a.hc)

# columns are re-ordered
heatmap.2(a, Rowv=a.de, Colv=FALSE)

# columns are re-ordered
heatmap.2(a, Rowv=a.de, Colv=1:5)

# columns are re-ordered
heatmap.2(a, Rowv=a.de, dendrogram="row")

# error
heatmap.2(a, Rowv=a.de, Colv=FALSE, dendrogram="row") 

Thanks in advance

Mick


	[[alternative HTML version deleted]]

On 3/6/06 9:19 AM, "michael watson (IAH-C)" <michael.watson at
bbsrc.ac.uk>
wrote:
> Hi
> 
> Sorry to revisit an old problem, I seemed to solve this in 2004, only
> for it to resurface :-S
> 
> I am trying to plot a heatmap, and I don't want the columns of my
matrix
> re-ordered.  The function doesn't seem to behave as the help would have
> you believe:
> 
> a <- matrix(rnorm(100),nr=20)
> a.d  <- dist(a)
> a.hc <- hclust(a.d)
> a.de <- as.dendrogram(a.hc)
> 
> # columns are re-ordered
> heatmap.2(a, Rowv=a.de, Colv=FALSE)
> 
> # columns are re-ordered
> heatmap.2(a, Rowv=a.de, Colv=1:5)
> 
> # columns are re-ordered
> heatmap.2(a, Rowv=a.de, dendrogram="row")
> 
> # error
> heatmap.2(a, Rowv=a.de, Colv=FALSE, dendrogram="row")
How about:

 heatmap.2(a,Rowv=a.de,Colv=1:5,dendrogram="row")

I thought Greg knew about this, but I'm not sure.  Have you updated gregmisc
recently?

Sean

We're just about to relase a version of gregmisc that improves the code and
documentation so that Rowv=FALSE and/or Colv=FALSE leaves the rows/columns in
the original order.

-G
> -----Original Message-----
> From: r-help-bounces at stat.math.ethz.ch
> [mailto:r-help-bounces at stat.math.ethz.ch]On Behalf Of Sean Davis
> Sent: Monday, March 06, 2006 9:25 AM
> To: michael watson (IAH-C); r-help
> Cc: Warnes, Gregory R
> Subject: Re: [R] Problems with heatmap.2 in the gregmisc package
> 
> 
> 
> 
> 
> On 3/6/06 9:19 AM, "michael watson (IAH-C)" 
> <michael.watson at bbsrc.ac.uk>
> wrote:
> 
> > Hi
> > 
> > Sorry to revisit an old problem, I seemed to solve this in 
> 2004, only
> > for it to resurface :-S
> > 
> > I am trying to plot a heatmap, and I don't want the columns 
> of my matrix
> > re-ordered.  The function doesn't seem to behave as the 
> help would have
> > you believe:
> > 
> > a <- matrix(rnorm(100),nr=20)
> > a.d  <- dist(a)
> > a.hc <- hclust(a.d)
> > a.de <- as.dendrogram(a.hc)
> > 
> > # columns are re-ordered
> > heatmap.2(a, Rowv=a.de, Colv=FALSE)
> > 
> > # columns are re-ordered
> > heatmap.2(a, Rowv=a.de, Colv=1:5)
> > 
> > # columns are re-ordered
> > heatmap.2(a, Rowv=a.de, dendrogram="row")
> > 
> > # error
> > heatmap.2(a, Rowv=a.de, Colv=FALSE, dendrogram="row")
> 
> How about:
> 
>  heatmap.2(a,Rowv=a.de,Colv=1:5,dendrogram="row")
> 
> I thought Greg knew about this, but I'm not sure.  Have you 
> updated gregmisc
> recently?
> 
> Sean
> 
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