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: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] Behalf Of [EMAIL PROTECTED] > Sent: Saturday, February 11, 2006 9:52 AM > To: r-devel@stat.math.ethz.ch > Cc: [EMAIL PROTECTED] > 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 > > ______________________________________________ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > ---------------------------------------------------------------------- LEGAL NOTICE\ Unless expressly stated otherwise, this messag...{{dropped}} ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
