Perhaps Bioconductor (or R for that matter) could have a "scripts" page,
where useful scripts could be uploaded for public use.

On Fri, Jul 23, 2010 at 5:04 AM, Steve Lianoglou <
mailinglist.honeypot@gmail.com> wrote:

> Hi,
>
> On Fri, Jul 23, 2010 at 6:44 AM, Benjamin Otto
> <b.otto@uke.uni-hamburg.de> wrote:
> > Hi Guys,
> >
> > thanks for confirmation. :-)
> >
> > I was pretty sure because I have a little modified script of heatmap.2()
> where I added some features such as scaling "before" clustering where I can
> choose between z-score or just median centering, or having the signal color
> legend below or beside the heatmap ... stuff like that. In fact it even has
> a little module which I snatched from the HeatPlus package (I remember it
> was called like that) that should provide the possibility to color the
> dendrogram-clusters according to a given parameter defining either number of
> clusters of cut-heigt.
> >
> > If somebody is interested just send me a notification. However I must
> warn you, that the modified code still has some minor bugs and is far from
> "package" ready, because I used to code it beside my projects and never had
> the time to concentrate on giving it a really final shape.
>
> Sure, why not? :-)
>
> Throw it up as a gist, perhaps, and those who like can hack it into shape:
> http://gist.github.com/
>
> I actually have my own version of heatmap.2 as well, because I'm
> convinced the default arguments in the function definition that deal
> with "symmetrical keys" are wrong.
>
> Take for instance the definition of the symbreaks argument:
> symbreaks = min(x < 0, na.rm=TRUE) || scale != "none"
>
> I'm pretty sure it should be `symbreaks = min(x, na.rm=TRUE) < 0 ||
> ...` since the former will always evaluate to 0 (FALSE)
> (likewise with symkey).
>
> I emailed the maintainer about it but never got a response, so I've
> just been using my own version since.
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact<http://cbio.mskcc.org/%7Elianos/contact>
>
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