[R] Problems with heatmap.2
michael watson (IAH-C)
michael.watson at bbsrc.ac.uk
Fri Sep 3 10:59:54 CEST 2004
Hi
I'm afraid not!
heatmap.2(as.matrix(d),Rowv=as.dendrogram(hc.gene),Colv=1:4,scale="row",
trace="none",col=greenred.colors(79))
Produces exactly the same results as if "Colv=FALSE" - my columns get
re-ordered (by a dendrogram no less). Clearly this isn't meant to be
happening.... (by the way, d is NOT a square matrix either)
Cheers
Mick
-----Original Message-----
From: Sean Davis [mailto:sdavis2 at mail.nih.gov]
Sent: 02 September 2004 14:39
To: michael watson (IAH-C)
Cc: r-help at stat.math.ethz.ch
Subject: Re: [R] Problems with heatmap.2
Didn't test this, but I think you probably want to do
dendrogram="row",Colv=1:n
where n is the number of samples.
Sean
On Sep 2, 2004, at 9:21 AM, michael watson (IAH-C) wrote:
> Hi
>
> When I give the command:
>
>>
> heatmap.2(as.matrix(d),Rowv=as.dendrogram(hc.gene),Colv=FALSE,scale="r
> o
> w
> ",trace="none",col=greenred.colors(79))
>
> The resulting heatmap has re-ordered my columns! This is time-course
> data, and I don't want my columns re-ordered! Note from the help:
>
> Rowv: determines if and how the _row_ dendrogram should be
> reordered. Either a 'dendrogram' or a vector of values used
> to reorder the row dendrogram or 'FALSE' to suppress
> reordering or by default, 'NULL', see _Details_ below.
>
> Colv: determines if and how the _column_ dendrogram should be
> reordered. Has the options as the 'Rowv' argument above and
> _additionally_ when 'x' is a square matrix, 'Colv = "Rowv"'
> means that columns should be treated identically to the
> rows.
>
> I have specifically set "Colv=FALSE" in my command.
>
> Help? What am I doing wrong?
>
> Cheers
> Mick
>
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