Re: [Rd] heatmap.2 in gplots (PR#8587)

From: Warnes, Gregory R <gregory.r.warnes_at_pfizer.com>
Date: Mon 13 Feb 2006 - 15:35:25 GMT


Nitin Jain and I are the maintainers of gplots. We'll look over the details of this bug report and correspond with Shane directly.

-G

> -----Original Message-----
> From: r-devel-bounces@r-project.org
> [mailto:r-devel-bounces@r-project.org]On Behalf Of dasnicht@mac.com
> Sent: Saturday, February 11, 2006 9:52 AM
> To: r-devel@stat.math.ethz.ch
> Cc: R-bugs@biostat.ku.dk
> Subject: [Rd] heatmap.2 in gplots (PR#8587)
>
>
> Full_Name: Shane Neph
> Version: 2.2.1
> OS: mac os x
> Submission from: (NULL) (71.113.43.247)
>
>
> While I found the names of the package authors and maintainer, I was
> unsuccessful in finding any contact information.
>
> The preliminary documentation for heatmap.2 is inconsistent
> in at least a couple
> of places when discussing the suppression of one or more
> dendrograms (and
> column/row ordering in general).
> In the Details section, in regards to the Rowv and Colv
> parameters, "If either
> is NULL, no reordering will be done for the corresponding
> side." The default
> value for these parameters is NULL. With NULL, the
> dendrograms are computed
> (and hence reordering is done).
> In the Arguments section, Rowv shows "determines if and how
> the row dendrogram
> should be reordered. Either a dendrogram or a vector of
> values to reorder the
> row dendrogram of FALSE to suppres reordering or by default,
> NULL, ...". In
> particular, the portion about FALSE should be contrasted with
> the portion about
> NULL in the Details section.
>
> Finally, it is my belief that part of the intention or using
> FALSE (or whatever
> is supposed to suppress the reordering) is to suppress the
> actual dendrogram
> drawing as well. This is similar to how NA works for the
> same argument names in
> the heatmap function. Achieving this behavior is
> straightforward. Assuming
> FALSE is the argument for suppression, the column
> dendrogram/reordering can be
> achieved by modifying heatmap.2 near line 78-80:
>
> FROM:
> else {
> colInd <- order(Colv)
> }
>
> TO:
> else if ( isTRUE(Colv) ) {
> colInd <- order(Colv)
> }
> else
> colInd <- 1:nc
>
> This does suppress the automatic column ordering/dendrogram
> as desired. Similar
> fixes for the Rowv argument are needed.
>
> R is great - keep up the work.
> Shane
>
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>



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