Hi Peter, Thanks for the advice and pointers to the relevant files. After reading the Fortran code and thinking about it I ended up coding from scratch my own pure R function to set the plotting order of an hclust object. It might not be as fast as the Fortran implementation, but it works pretty well and as far as I can tell the resulting order is exactly the same to the original hclust code. If anyone is interested it's available at the CopyNumberPlots package at https://github.com/bernatgel/CopyNumberPlots/blob/5b9a1efea53e424a32616b7d82560d81c9ba4a10/R/utils.R#L933
Bernat El 8/3/19 a las 8:41 PM, Peter Langfelder escribió: > Hi Bernat, > > my advice may not be that useful, but it may be better than the > silence so far... > > Regarding the ordering of objects in hclust, if you're willing to do a > bit of hacking, have a look at the stats::hclust function; you will > see that the ordering is computed by a call to Fortran function > hcass2. That function could be used or perhaps adapted (it uses an > additional step that you will probably need to skip) to give you the > ordering. If you're good at understanding Fortran code, you may even > be able to re-write it directly in R. > > Peter > > On Tue, Jul 30, 2019 at 12:39 AM Bernat Gel Moreno <b...@igtp.cat> wrote: >> Hi, >> >> For one of our packages (CopyNumberPlots) we'll need to read 10X CNV >> data in H5 format. I've read in everything I need except for the cell >> clustering tree. It's in a format called Z format produced by SciPy >> hierarchical clustering. The format itself is relatively easy to parse >> and not so different from hclust return objects so it would be possible >> to create a small function to translate the Z notation into an hclust >> object, if needed, but I'll need to figure out the "order" vector, since >> it's not present in Z. >> >> - Is the Z to hclust function available in any other package? Or >> something equivalent to that? >> - If I end up transforming it by hand in a custom function, Is there >> a function somewhere to compute the order vector in an hclust object? >> >> Thanks >> >> Bernat >> >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
