[BioC] specifying hyperlinks on the plot

Vincent Carey 525-2265 stvjc@channing.harvard.edu
Sat, 2 Nov 2002 10:08:32 -0500 (EST)


>
> Hi,
>
> is there a capability in R/bioconductor for specifying hyperlinks from a ,
> say, postscript or pdf plot. For instance, when I produce n by p image
> matrix with log2ratios and with all the clone names for the columns
> listed, is there a way to create a mark-up so that by clicking on a clone
> name to be taken to golden path (UCSC) info on the clone?

the short answer is no.  a related question is why restrict to pdf
or postscript?  for x11 graphics, the locator function can be used
to get information about mouse position.

in my view the idea of specifying hyperlinks from a plot needs
to be decomposed.  problem 1 is getting useful info on mouse
position.  this requires some approximation because the user
may not have good aim.  problem 2 is translating info on mouse
position to info about clone identity.  problem 3 is getting
from clone identity to golden path.  problems 1 and 3 have
solutions in R/bioconductor, and problem 2 does not seem
so hard.  but one could also entertain the idea of encoding
hyperlink information in pdf with each spot.  that idea
is unattractive to me but it is closer to the intent of your
question and i think it is possible.  i would look at the
hyperlink encoding capabilities of pdflatex for a start.

to get started on the other approach, a function like

function(apx=round) {  apx(unlist(locator(1)),0); }

will with the default setting of apx give you the integer
coordinates closest to the mouse click on an R x11 device.
if you have really good aim, set apx=function(x)x ... that
setting of apx will also be useful if the coordinate processing
is done under the hood.

>
> If that is not possible, what would be the closest thing which is
> implemented?
>
> Thank you
>
>
> Jane
>
>
>
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> UCSF Cancer Center, Box 0128 San Francisco, CA 94143-0128
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