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

[Warnes, Gregory R]

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 at r-project.org
> [mailto:r-devel-bounces at r-project.org]On Behalf Of dasnicht at mac.com
> Sent: Saturday, February 11, 2006 9:52 AM
> To: r-devel at stat.math.ethz.ch
> Cc: R-bugs at 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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