heatmap.2 in gplots (PR#8587)

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heatmap.2 in gplots (PR#8587)

dasnicht
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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Re: heatmap.2 in gplots (PR#8587)

Uwe Ligges
[hidden email] wrote:

> 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.

This is not a bug in R, hence please do not post it to R-bugs, R-devel
would have been much more appropriate.
You will get contact information of the maintainer by typing, e.g.:

  library(help=gplots)

Uwe Ligges



> 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
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

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

Warnes, Gregory R
In reply to this post by dasnicht
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: [hidden email]
> [mailto:[hidden email]]On Behalf Of [hidden email]
> Sent: Saturday, February 11, 2006 9:52 AM
> To: [hidden email]
> Cc: [hidden email]
> 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
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
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