[BioC] specifying hyperlinks on the plot

[Vincent Carey 525-2265]

On Sat, 2 Nov 2002, Byron Ellis wrote:

>
> On Saturday, November 2, 2002, at 01:55  PM, A.J. Rossini wrote:
>
> >
> >     vincent> the short answer is no.  a related question is why
> > restrict to pdf
> >     vincent> or postscript?  for x11 graphics, the locator function
> > can be used
> >     vincent> to get information about mouse position.
> >
> > Restriction may be the wrong word, but the general idea is solid, I
> > think (i.e. mailing a hyperlinked PDF file to collaborators, for
> > example).
> >
>
> Even beyond this, PDF also supports embedded Javascript (for better or
> for worse) that could let you do potentially interesting things. Being
> able to generate active PDFs is definitely desirable (for posting or
> mailing to people who neither know nor care about R :-)). I don't see
> the current device driver model handling this very well.

ok, i am warming up to this idea, but i suspect that the density
of hyperlinks to be handled by existing designs would be pretty
light (at most a few links per line of narrative text or per embedded image).
what jane is describing sounds very dense, and the quantity of
metadata in a chip image could be substantial even if only one
sort of link resolution were required ([x,y] to locuslink, e.g.).
one would want to do the mapping from the geometry of the document
(image) to the genomic annotation outside the document -- so i
would assume that the document and a database would be involved
at a minimum.

i made a cursory search on active pdf and a check of the adobe
site.  i don't see anything immediately available for prototyping.
one approach is to generate the pdf image in R and then apply
some adobe tool to introduce a hyperlink.  i would assume distiller
could do this but i do not have access.  if this worked we would
then consider how best links could be introduced en masse.