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

[dasnicht@mac.com]

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